World Index of BioMolecular Visualization Resources
World Index of BioMolecular Visualization Resources
Biochemical Structure Tutorials
Titles Subjects Authors: Detailed Compact HOME
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2,3-bisphosphoglycerate (BPG) :
Oxygen Binding Proteins: Myoglobin and Hemoglobin. (Reichsman, Frieda; Driscoll, Timothy)
2-phosphoenolpyruvate :
The Glycolytic Cycle. (Warren, L. Van)
2-phosphoglycerate :
The Glycolytic Cycle. (Warren, L. Van)
3-phosphoglycerate :
The Glycolytic Cycle. (Warren, L. Van)
Top 0 1 2 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
30S ribosomal subunit :
Ribosome Tour. (Decatur, Wayne)
30S ribosomal subunit :
70S Ribosome Architecture. (McClure, Will)
3D Periodic Table of Radii:
Cross-indexing terms: periodic table of the elements; elements, periodic table of; atomic radii; trends, periodic, in atomic and ionic sizes.
This image displays the elements as spheres arranged as in the periodic table. The spheres have sizes proportional to the atomic, ionic and van der Waals radii. The different neutral and ionic states are presented on different planes. The site is designed to be viewed with Chime and there is also a set of buttons to create displays of only particular planes, elements, groups, periods, and coloring schemes. The primary application is for a discussion of periodic trends in atomic and ionic size.
Author: Wherland, Scot Submitted by: the author. (Entry 70). Submitted on Nov 1, 2000.
3DEE :
XdomView: A Chime-based Graphical Tool for Protein Domain and Exon Position Visualization. (Gopalan, Vivek; Shoba Ranganathan; Tan Tin Wee)
434 repressor :
Protein/DNA interactions. (Gibson, Andrew; Sims, P. F. G.)
Top 0 1 2 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
50S ribosomal subunit :
Ribosome Tour. (Decatur, Wayne)
50S ribosomal subunit :
Large Ribosomal Subunit Tour. (Decatur, Wayne)
50S ribosomal subunit :
70S Ribosome Architecture. (McClure, Will)
70S Ribosome architecture :
Ribosome Tour. (Decatur, Wayne)
70S Ribosome architecture :
70S Ribosome Architecture. (McClure, Will)
A-DNA :
Biomodel. (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish)
A-DNA :
DNA Conformers (at The Online Macromolecular Museum). (Marcey, David)
A-Form RNA helix :
Structures for Molecular Biology. (McClure, William)
Top 0 1 2 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
α-Helix & β-Sheet in a Small Protein :
Molecules for Modern/Cell Biology. (McClure, William)
α-lactalbumin (1b90.pdb), a human plasma transport protein :
Protein Structures List. (McClure, William)
access to the active site :
Rubisco: a first look at the mechanism. An experiment in molecular visualisation. (Nixon, John)
Accessible, molecular and Van der Waals surfaces explained:
Cross-indexing terms: surfaces; solvent accessible surface; molecular surface; van der Waals surface; YASARA.
An introduction to protein surfaces, explaining the difference between solvent accessible, molecular and Van der Waals surface. Shows water molecules rolling across the protein. Advanced tutorials about surface area calculations are available from the same page. The tutorial requires (and comes with) YASARA View.
Author: Krieger, Elmar Submitted by: the author. (Entry 152). Submitted on Aug 13, 2004.
Top 0 1 2 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
acesulfame :
Everything You Ever Wanted to Know about Sweeteners. (Walters, D. Eric)
acetycholinesterase-edrophonium :
Molecular Science Lab. (Oberholser, Karl)
Acetyl-CoA :
Isoprenoid Biosynthesis Pathway. (Warren, L. Van)
acetylcholinesterase inhibitors :
Molecular Science Lab. (Oberholser, Karl)
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acetylcholinesterase mechanism :
Molecular Science Lab. (Oberholser, Karl)
acetylcholinesterase- m-(N,N,N-trimethylammonio)trifluoroacetophenone :
Molecular Science Lab. (Oberholser, Karl)
acetylcholinesterase-decamethonium :
Molecular Science Lab. (Oberholser, Karl)
acetylcholinesterase-tacrine :
Molecular Science Lab. (Oberholser, Karl)
Top 0 1 2 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
actinomycin :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
activators :
Chime Square. (Niederhoffer, Eric)
active site :
Carboxypeptidase A - Three Exercises with Chime. (Morgan, Eleanor; Helmerhorst, Erik)
Adenosine Kinase :
The Lycoming College Macromolecular Modeling and Bioinformatics Page. (Newman, Jeff)
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Adenosine Triphosphate :
Molecule of the Month/University of Bristol. (May, Paul (editor))
ADP :
The Glycolytic Cycle. (Warren, L. Van)
Adrenaline :
Molecule of the Month/University of Bristol. (May, Paul (editor))
Advanced Protein Explorer :
Protein Explorer, Advanced. (Martz, Eric; (MSA3D component coauthored by Paul Stothard))
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Aequoria victoria :
GFP (Green Fluorescent Protein). (Driscoll, Timothy)
AHo's Amazing Atlas of Antibody Structure:
Cross-indexing terms: antibody; antibodies; multiple sequence alignment; sequence variability; homology modelling; immunoglobulin; domains; color-coded multiple sequence alignment.
This site contains extensive tutorials and lectures on antibody structure coupled with analyses of sequence variability in antibodies. The site also has a very nice set of Microsoft EXCEL spreadsheets with macros that are very useful in displaying and analyzing protein multiple sequence alignments. The Numbering pages contain descriptions and help with the various schemes that have been applied to numbering amino acid positions within antibody molecules. Other pages contain extensive pre-built color-coded multiple sequence alignments which illustrate the usefulness of the EXCEL macros. There are CHIME based 3D structure displays and diagrams of antibody structures available.
Author: Honegger, Annemarie Submitted by: Foley, Brian. (Entry 157). Submitted on Oct 12, 2004.
AIDS :
BioMolecular Explorer 3D: Resources for High School Biology. (Reichsman, Frieda; Eric Martz)
albumin :
Garrett & Grisham Interactive Biochemistry. (Garrett, R. H.; Grisham, C. M.)
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albumin, serum :
Garrett and Grisham Interactive Biochemistry Structure Tutorials. (Caras, James)
aldolase :
The Glycolytic Cycle. (Warren, L. Van)
alignment :
Structural Alignment Program for Proteins. (Gille, Christoph)
Alkaline phosphatase:
Cross-indexing terms: alkaline phosphatase; enzyme-substrate complex.
A lecture-oriented chime 'slide show' about alkaline phosphatase. Buttons show particular views (these must usually be played in order) and a caption appears in the lowest frame. This shows
• the two subunits with active sites highlighted & substrate added
• a close-up of the active site with critical substrate-enzyme bonds
Author: White, Brian Submitted by: the author. (Entry 79). Submitted on Nov 10, 2000.
Alkaline phosphatase:
Cross-indexing terms: alkaline phosphatase; enzyme-substrate complex.
A lecture-oriented chime 'slide show' about alkaline phosphatase. Buttons show particular views (these must usually be played in order) and a caption appears in the lowest frame. This shows
• the two subunits with active sites highlighted & substrate added
• a close-up of the active site with critical substrate-enzyme bonds
Author: White, Brian Submitted by: the author. (Entry 79). Submitted on Nov 10, 2000.
Top 0 1 2 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
Alkohole, Kohlenhydrate, Carbonsaeuren, Aminosaeuren, Eiweisse :
Chemie und Internet am Gymnasium. (Rausch, Martin) (German)
alpha helix :
Protein Secondary Structure, versions 1.0, 2.0, 3.0. (Reichsman, Frieda; Driscoll, Tim)
alpha helix :
Introduction to Protein Structure. (Gorga, Frank)
alpha-helix :
Introduction to Protein Structure, Part I. (Bragin, Victoria (Vicki))
alpha-helix :
Biomodel. (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish)
alpha-helix :
Animations on subjects of Structural and Metabolic Biochemistry. (Silva, Pedro)
Alzheimer's :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
Top 0 1 2 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
amino acid :
Molecules and Structures Homepage. (Gasser, Charles)
amino acid chemistry :
Introduction to Protein Structure. (Gorga, Frank)
Amino Acid Identification Quiz:
Cross-indexing terms: lesson plan; quiz; amino acids.
Quiz in a frames format; the user is required to identify the 20 amino acids shown as Chime images by name, abbreviation, and/or one-letter code. Answers are provided after each selection, and a running total of correct and incorrect responses is tabulated.
Author: McClure, William Submitted by: the author. (Entry 28). Submitted on Jun 1, 2000.
Amino Acid Quizzer:
Cross-indexing terms: quizzer, amino acid; lesson plan, amino acid quizzer.
At : The wireframe of a small protein is shown in Chime. Each student is assigned a residue number or range. When the number(s) are entered, Chime automatically zooms in to show atomic detail of the amino acid(s) as ball and stick, CPK-colored (color key is provided). Students can then answer questions posed by the instructor such as amino acid identity, side-chain properties, and which of two amino acids is closer to the N terminus. Lesson plan (sequence key is available to instructors on request). Downloadable for off-line use, local installation or modification.
Authors: Martz, Eric; White, Brian. Submitted by: the author. (Entry 17). Submitted on May 28, 2000. Last revised on Oct 3, 2004.
Amino Acid Quizzer :
Small Molecule Lab Exercise. (White, Brian)
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Amino Acid Structure Quiz:
Cross-indexing terms: quiz, amino acid structure; lesson plan.
Fifteen questions that cover all 20 amino acids, answered by clicking on the correct atoms in static snapshots of spacefilling or ball-and-stick models. Hints are available.
Author: McClure, William Submitted by: Martz, Eric. (Entry 149). Submitted on May 16, 2004.
Amino Acid Structures :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
amino acids :
Protein Architecture at Biochemistry in 3D. (Driscoll, Timothy; Reichsman, Frieda)
amino acids :
Amino Acid Identification Quiz. (McClure, William)
amino acids :
Course Home Page for "Computer Applications in Biotechnology". (Klevickis, Cindy)
amino acids :
Sickle Cell Anemia: Understanding the Molecular Biology. (Sabo, John; Lynch, Jamie; Raineri, Deanna)
amino acids :
Biomodel. (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish)
amino acids :
Biomolecular Structures. (Hansson, Orjan)
Amino Acids & Peptides :
Molecules for Modern/Cell Biology. (McClure, William)
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amino acids and properties :
The 20 common amino acids. (Bragin, Victoria (Vicki); Johnston, Wendie)
amino acids, all 20 :
Side-by-Side Amino Acid Viewer. (McClure, William)
aminoacyl-tRNA synthetase :
Biomodel. (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish)
Anatoxin :
Molecule of the Month/University of Bristol. (May, Paul (editor))
Top 0 1 2 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
animated gifs :
Course Home Page for "Computer Applications in Biotechnology". (Klevickis, Cindy)
animation of translation in the ribosome :
70S Ribosome Architecture. (McClure, Will)
animation with XYZ files :
Thermal motion of alpha helix. (Cachau, Raul E.)
animations :
Lac repressor bending DNA operon. (Martz, Eric)
Top 0 1 2 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
animations of vibrations, infrared spectra :
Infrared spectra, animations of vibrational modes. (Motyka, Eric; Lahti, Paul; Lancashire, Robert J.)
Animations on subjects of Structural and Metabolic Biochemistry:
Cross-indexing terms: alpha-helix; beta-sheet; oxyhemoglobin; deoxyhemoglobin; cytochrome c oxidase; succinate dehydrogenase; cytochrome bc1; respiratory chain complexers; electron transport chain.
Chime-based tutorials on protein secondary, structure, hemoglobin and electron-transfer complexes. More will eventually follow.
Author: Silva, Pedro Submitted by: the author. (Entry 148). Submitted on Mar 15, 2004. Last revised on Mar 15, 2004.
antibiotics :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
antibodies :
AHo's Amazing Atlas of Antibody Structure. (Honegger, Annemarie)
Top 0 1 2 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
Antibody:
Cross-indexing terms: immunoglobulin and Ig domains; IgG; epitope structure, lysozyme bound to antibody; disulfide bonds in immunoglobulin; complementarity-determining regions in antibody; glycosylation of antibody, N-linked; lesson plan, antibody.
At : A tutorial on IgG structure in Chime including an introduction to stick, ball and stick, spacefill renderings, peptides and backbones, disulfide bond renderings, the immunoglobulin domain (secondary structure, disulfide bond, hydrophobic core and polar surface), Fab:lysozyme complex with all 6 CDR's identified, paratope contact atoms vs. CDR's, epitope contact atoms, the flat and discontinuous character of the epitope, F(ab')2 and inter-chain disulfide bonds, intact IgG1, and the location and attachment of carbohydrate. Buttons can be pushed in any order yet always give the same images. Font size can be dymanically changed for large audiences. The utilities menu enables recentering, atom identification, measuring distances, and changing background color from black to white for printing. A list of questions is provided which can be printed and handed out to a class as a focus worksheet (lesson plan). Downloadable for off-line use, local installation or modification.
Author: Martz, Eric Submitted by: the author. (Entry 14). Submitted on May 28, 2000. Last revised on Oct 3, 2004.
Antibody :
AHo's Amazing Atlas of Antibody Structure. (Honegger, Annemarie)
Antibody :
BioMolecular Explorer 3D: Resources for High School Biology. (Reichsman, Frieda; Eric Martz)
Antibody Recognition of Antigen :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
Antibody Recognition of Antigen (at The Online Macromolecular Museum):
Cross-indexing terms: hypervariable regions, immunoglobulin; immunoglogulin binding; complementarity-determining regions; CDRs.
This exhibit uses three examples of antibody-antigen complexes to illustrate some structural features of antibody recognition of epitope. Antibody bound to a globular protein antigen is followed by an examination of the mechanisms of peptide antigen binding. The exhibit finishes with a look at antibody recognition of a small antigenic molecule, a hapten.
Author: Marcey, David Submitted by: the author. (Entry 115). Submitted on Jun 18, 2001.
antibody structure :
Immunoglobulin Structure (at The Online Macromolecular Museum). (Marcey, David)
Top 0 1 2 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
antiparallel strands :
DNA Structure (at The Online Macromolecular Museum). (Marcey, David)
apoptosis, programmed cell death, caspases, NF-kappa B, Ik-B, bcl-2, IAP :
Molecular Visualizations on Apoptosis. (Pons, Gabriel; Gil, Joan) (Spanish)
AQP1 Aquaporin Channel (1j4n.pdb) :
Membrane Channel & Pump Structures. (McClure, William)
archaeal rhodopsins :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
Top 0 1 2 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
aromatic sidechains: face-to-face, side-to-face, face-to-cation :
Noncovalent Interactions in Proteins. (Cox, Ricky)
ASBMB :
. (Biochemistry and Molecular Biology, American Society of)
aspartame :
Everything You Ever Wanted to Know about Sweeteners. (Walters, D. Eric)
AT base pair :
DNA Structure. (Martz, Eric) (English, German, Portuguese, Spanish)
AT base pair :
DNA Structure (with Jmol). (Herraez, Angel; Martz, Eric)
Top 0 1 2 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
atomic radii :
3D Periodic Table of Radii. (Wherland, Scot)
ATP :
Molecule of the Month/University of Bristol. (May, Paul (editor))
ATP :
Molecules for Modern/Cell Biology. (McClure, William)
ATP :
The Glycolytic Cycle. (Warren, L. Van)
authoring new Chime websites, methods :
How to Create New Chime Tutorials. (Martz, Eric)
azt :
HIV-1 Reverse Transcriptase (at The Online Macromolecular Museum). (Goldman, Matthew; Marcey, David)
Top 0 1 2 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
B-DNA :
Biomodel. (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish)
B-DNA :
DNA Conformers (at The Online Macromolecular Museum). (Marcey, David)
B-DNA :
DNA Structure (at The Online Macromolecular Museum). (Marcey, David)
B-Form Deoxyribonucleic Acid (DNA):
Cross-indexing terms: deoxyribonucleic acid, DNA, major groove, minor groove.
This Chime resource contains animations to illustrate the structure of DNA. The animations are initiated by clicking buttons on the right pannel. They show a base pair in the context of a larger helix and highlight the bases, sugars and phosphates. You can see how the helix is created by observing the structure of a two and three base pair helix. The last animation emphasizes how the major and minor grooves are created. The DNA coordinates were generated by Sybyl using idealized coordinates for B-DNA.
Author: Bruist, Michael Submitted by: the author. (Entry 85). Submitted on Jan 19, 2001.
B-Form DNA helix :
Structures for Molecular Biology. (McClure, William)
bacterial photosynthesis :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
Top 0 1 2 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
bacteriophage cro :
Cro Repressor of Temperate Bacteriophages (at The Online Macromolecular Museum). (Marcey, David)
bacteriophage repressor :
Cro Repressor of Temperate Bacteriophages (at The Online Macromolecular Museum). (Marcey, David)
Bacteriorhodopsin:
Cross-indexing terms: bacteriorhodopsin (1brx.pdb).
A one-page Chime display of nine recent bacteriorhodopsin structures and links to the PubMed entries for the structure references.
Author: McClure, William Submitted by: the author. (Entry 24). Submitted on Jun 1, 2000.
bacteriorhodopsin (1brx.pdb) :
Bacteriorhodopsin. (McClure, William)
Top 0 1 2 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
Bacteriorhodopsin (1c3w.pdb, 1dze.pdb) :
Membrane Channel & Pump Structures. (McClure, William)
Bacteriorhodopsin (Br.pdb), a light-driven proton pump :
Protein Structures List. (McClure, William)
Bacteriorhodopsin: A membrane-spanning protein :
Molecules for Modern/Cell Biology. (McClure, William)
BamHI endonuclease :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
Top 0 1 2 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
BamHI Restriction Endonuclease (at The Online Macromolecular Museum):
Cross-indexing terms: Type II restriction endonuclease; restriction enzymes; DNA-binding protein; DNA cleavage.
BamHI is a type II restriction endonuclease, having the capacity for recognizing short sequences (6 b.p.) of DNA and specifically cleaving them at a target site. This Chime-based exhibit focuses on the structure-function relationships of BamHI.
Authors: Silva, Nathan; Leslie, Kenneth; Marcey, David. Submitted by: Marcey, David. (Entry 100). Submitted on Jun 17, 2001.
base pairing :
Sickle Cell Anemia: Understanding the Molecular Biology. (Sabo, John; Lynch, Jamie; Raineri, Deanna)
base pairs :
DNA Structure. (Reichsman, Frieda) (English, Italian)
basic biochemistry for undergrads :
Biomolecular Structures. (Hansson, Orjan)
Top 0 1 2 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
Bence-Jones protein REI monomer & dimer :
Molecular Science Lab. (Oberholser, Karl)
bending of DNA :
Lac repressor bending DNA operon. (Martz, Eric)
beta barrel :
GFP (Green Fluorescent Protein). (Driscoll, Timothy)
beta pleats :
Introduction to Protein Structure, Part I. (Bragin, Victoria (Vicki))
Top 0 1 2 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
beta sheet :
Protein Secondary Structure, versions 1.0, 2.0, 3.0. (Reichsman, Frieda; Driscoll, Tim)
beta sheet :
Introduction to Protein Structure. (Gorga, Frank)
beta-elimination :
Rubisco: a first look at the mechanism. An experiment in molecular visualisation. (Nixon, John)
beta-sheet :
Biomodel. (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish)
beta-sheet :
Animations on subjects of Structural and Metabolic Biochemistry. (Silva, Pedro)
bilayer, lipid :
Biomodel. (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish)
bilayer, lipid :
Lipid Bilayers and the Gramicidin Channel. (Martz, Eric; Herraez, Angel)
Top 0 1 2 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
BioEditor :
Zinc Binuclear Clusters. (Craig, Paul)
Biomodel: (Spanish )
Cross-indexing terms: amino acids; peptides; proteins; alpha-helix; beta-sheet; collagen; hemoglobin; immunoglobulin; DNA; A-DNA; B-DNA; Z-DNA; RNA; rRNA; tRNA; nucleosome; helix-turn-helix; helix-loop-helix; homeodomain; leucine zipper; zinc finger; aminoacyl-tRNA synthetase; bilayer, lipid; lipid bilayer; gramicidin channel; rybozymes; Rev protein; RBE; EF-Tu; U1A; spliceosome.
Self-guided tutorial, emphasizing 3D-structure and interaction between macromolecules. It is in Spanish. Runs as Chime models inside an explanatory web page. Allows both guided tour and user-chosen pathway and action on models. Biomodel-1 covers amino acids, peptides, secondary, tertiary and quaternary structure of proteins (exemplified by alpha-helix, beta-sheets, collagen, hemoglobin and immunoglobulins), DNA (A-, B- and Z- forms), RNA, and interactions of nucleic acids with protein motifs (nucleosome, helix-turn-helix, helix-loop-helix, homeodomain, leucine zipper, zinc finger, and RNA-protein complexes). Addressed to University students of Biochemistry and Molecular Biology. Biomodel-2: a Chime version of Eric Martz's Rasmol script on bilayer membranes and gramicidin channel. Biomodel-3 is a lower-level module addressed to secondary school students, includes sugars, lipids, some vitamins, amino acids, proteins, bases, nucleosides, nucleotides and nucleic acids.
Authors: Herraez, Angel; Lopez-Lopez, Jose Ramon. Submitted by: the author. (Entry 89). Submitted on Mar 13, 2001. Last revised on Jul 8, 2002.
BioMolecular Explorer 3D: Resources for High School Biology:
Cross-indexing terms: antibody; collagen; DNA; hemoglobin; HIV; protease; protease inhibitor; HIV-protease inhibitor; AIDS; lactase; lac repressor; lipid bilayers; myosin; nucleosome; water; high school; high school biology; lesson plan; Chime.
BioMolecular Explorer 3D is a website designed to provide high school teachers with interactive 3D structures of biologically significant molecules that fit in high school biology curricula.
The following resources are available at BioMolecular Explorer 3D:
1. Links to software for viewing and exploring molecules in 3D
o download the software
o follow our instructions for installing it
2. Pre-selected biomolecules that fit well in a high school biology curriculum
o each molecule is placed in its biological context with a brief description
o each molecule is linked to an interactive 3D display (assuming prior installation of software)
3. Assistance with lesson planning
o each molecule is linked to background information specially selected for HS teachers
4. Access to additional molecules
o we show you where to find many other biomolecular 3D displays and tutorials
Authors: Reichsman, Frieda; Eric Martz. Submitted by: the author. (Entry 160). Submitted on Dec 14, 2004.
Biomolecular Structures:
Cross-indexing terms: amino acids; peptides; basic biochemistry for undergrads; protein structure; nucleotides; DNA; RNA; lesson plan.
Biomolecular Structures is an Internet tutorial intended as a computer-based laboratory exercise for undergraduate students in basic biochemistry. It covers the basic properties of amino acids, peptides, proteins, nucleotides and nucleic acids. The tutorial makes use of the Chemscape Chime plug-in and JavaScript. Particular attention has been paid to the design of the user interface so that students which are not so experienced with computers can navigate easily through the course. A form with simple questions is included. Extensive help is available to guide the user.
Author: Hansson, Orjan Submitted by: the author. (Entry 132). Submitted on Jun 7, 2002. Last revised on Jun 7, 2002.
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Biomolecules at Kenyon College: (English; CopG auf Deutch )
Cross-indexing terms: Tc3 transposase; NS3 protease; HIV-1 dimer; hemoglobin; CopG; Catabolite activator protein; tRNA synthetase; lac repressor; HIV reverse transcriptase.
Biomolecules at Kenyon College presents Chime tutorials which illustrate the structure and function of biomolecules using PDB files from the Protein Data Bank. Gene regulators are complexed with DNA binding sites; cytoplasmic molecules are also presented. Examples include: Tc3 transposase, catabolic activator protein, tRNA synthetase, fibronectin, and hemoglobin. CopG includes a German version; future alternative language versions are planned. All tutorials are authored by Kenyon College undergraduates in the advanced molecular biology course.
Authors: Students, Kenyon College; Site Director, Joan Slonczewski. Submitted by: Slonczewski, Joan. (Entry 84). Submitted on Jan 4, 2001. Last revised on Jan 9, 2001.
:
Cross-indexing terms: ASBMB; curriculum resources for biochemistry.
Features free, downloadable, peer-reviewed educational resources including Software, Visual Resources, Curriculum Resources, Articles and Reviews for Biochemistry and Molecular Biology Education. Site users can submit new resources subject to peer review. Sponsored by the American Society of Biochemistry and Molecular Biology.
Author: Biochemistry and Molecular Biology, American Society of Submitted by: Martz, Eric. (Entry 155). Submitted on Oct 2, 2004.
BLAST :
XdomView: A Chime-based Graphical Tool for Protein Domain and Exon Position Visualization. (Gopalan, Vivek; Shoba Ranganathan; Tan Tin Wee)
blood coagulation :
Structural Biochemistry of Blood Coagulation. (Walters, D. Eric)
Top 0 1 2 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
Boswellic Acid :
Molecule of the Month/University of Bristol. (May, Paul (editor))
Bowen's Reaction Series :
Molecular Visualization Resources for Project VISM. (Klevickis, Cindy)
BPTI :
Molecular Science Lab. (Oberholser, Karl)
Bupropion :
Molecule of the Month/University of Bristol. (May, Paul (editor))
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C-helix :
Cytochrome P450 3D structures page. (Nelson, David)
calcium binding to an EF-hand, morph :
Morpher, Protein. (Martz, Eric)
calmodulin, morphs :
Morpher, Protein. (Martz, Eric)
cAMP :
Molecules for Modern/Cell Biology. (McClure, William)
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cAMP kinase, morph :
Morpher, Protein. (Martz, Eric)
cAMP Receptor Protein (CRP) :
Structures for Molecular Biology. (McClure, William)
CAP (cAMP binding protein) & DNA :
Molecules for Modern/Cell Biology. (McClure, William)
carbamate :
Rubisco: a first look at the mechanism. An experiment in molecular visualisation. (Nixon, John)
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carbon fixation :
Rubisco: a first look at the mechanism. An experiment in molecular visualisation. (Nixon, John)
carboxylase :
Rubisco: a first look at the mechanism. An experiment in molecular visualisation. (Nixon, John)
Carboxypeptidase :
Carboxypeptidase A - Three Exercises with Chime. (Morgan, Eleanor; Helmerhorst, Erik)
carboxypeptidase A :
Carboxypeptidase A - Three Exercises with Chime. (Morgan, Eleanor; Helmerhorst, Erik)
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Carboxypeptidase A - Three Exercises with Chime:
Cross-indexing terms: Carboxypeptidase; protein structure; enzyme active site; carboxypeptidase A; carboxypeptidase enzyme; active site; quiz question interface.
In this tutorial, students will be looking at the enzyme Carboxypeptidase A using the Chemscape Chime plug-in. This plug-in is very similar in functionality to Rasmol - an interactive Molecular Visualisation program. A previous version (still available) of this tutorial was designed to use the RasMol program as a web helper application.We have attempted to design the Chime version of these tutorials so that students will also feel comfortable using RasMol afterwards if they wish to. In order to use the Rasmol interactive program effectively, you must type in many of the commands at the Rasmol prompt in the command window.We have preserved this interactivity by creating a 'command line' text box in which you can send commands to theChime Plug-in. Many thanks go to Eric Martz (creator of the RasMol/Chime website) for providing usefulJavaScript examples which showed us how to do this. The tutorials also contain interactive questions which employ JavaScript to check the answers. There are three exercises in the tutorial. The first serves as an introduction to the use of Chime, a second which looks primarily at the secondary structure of proteins, and a third which explores the active site of Carboxypeptidase.
Authors: Morgan, Eleanor; Helmerhorst, Erik. Submitted by: the author. (Entry 47). Submitted on Jul 17, 2000.
carboxypeptidase enzyme :
Carboxypeptidase A - Three Exercises with Chime. (Morgan, Eleanor; Helmerhorst, Erik)
casein kinase II :
Protein Kinase CKII. (Glover III, Claiborne)
Catabolite activator protein :
Biomolecules at Kenyon College. (Students, Kenyon College; Site Director, Joan Slonczewski) (English; CopG auf Deutch)
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Catalase :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
Catalase (at The Online Macromolecular Museum):
Cross-indexing terms: oxidoreductase; hydrogen peroxide.
Catalase, present in the peroxisomes of nearly all aerobic cells, serves to protect the cell from the toxic effects of hydrogen peroxide by catalyzing its decomposition into molecular oxygen and water without the production of free radicals. This Chime-based exhibit explores structure-function relationships of this important oxidoreductase.
Authors: Boon, Elizabeth; Downs, Aaron; Marcey, David. Submitted by: Marcey, David. (Entry 97). Submitted on Jun 17, 2001.
catalytic RNA :
Nucleic Acid Structure Tutorials. (Nolan, Jim)
CATH :
XdomView: A Chime-based Graphical Tool for Protein Domain and Exon Position Visualization. (Gopalan, Vivek; Shoba Ranganathan; Tan Tin Wee)
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cation-pi interactions :
Noncovalent Interactions in Proteins. (Cox, Ricky)
CD4 downregulation :
HIV-1 Nef Protein (at The Online Macromolecular Museum). (Somple, Maggie; Silva, Nathan; Marcey, David)
CDRs :
Antibody Recognition of Antigen (at The Online Macromolecular Museum). (Marcey, David)
Chemical Bonds and Protein Structure (at The Online Macromolecular Museum):
Cross-indexing terms: chymotrypsin; hydrogen bonds; ionic bonds; salt bridges; hydrophobic bonds; noncovalent bonds; Van der Waals forces.
This Chime-based exhibit shows a few examples of the types of chemical bonds that play important roles in forming and stabilizing macromolecular structure. A model peptide of 12 amino acids that spans the gamma chymotrypsin protein is used to illustrate example bonds in a known structure.
Author: Marcey, David Submitted by: the author. (Entry 96). Submitted on Jun 17, 2001. Last revised on Jun 18, 2001.
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Chemie und Internet am Gymnasium: (German )
Cross-indexing terms: Alkohole, Kohlenhydrate, Carbonsaeuren, Aminosaeuren, Eiweisse.
Lernumgebungen mit CHIME und Skriptsteuerung:
• Alkohole
• Kohlenhydrate
• Carbonsaeuren
• Aminosaeuren und Eiweisse
Author: Rausch, Martin Submitted by: the author. (Entry 66). Submitted on Aug 30, 2000. Last revised on Aug 31, 2000.
ChemSymphony :
Molecule of the Month/University of Bristol. (May, Paul (editor))
Chime :
Water Simulation. (Martz, Eric)
Chime :
Lac repressor bending DNA operon. (Martz, Eric)
Chime :
BioMolecular Explorer 3D: Resources for High School Biology. (Reichsman, Frieda; Eric Martz)
Chime 2 Tutorial:
A tutorial in Chime 2 on how to use Chime 2. Includes sections on how to use the mouse, buttons, change the center of rotation, change the appearance, change the color, measure a distance, select a subset for coloring, save files and images, see a molecule in stereo, have RasMol-like functionality with javascript. Also included are links to Chime-based tutorials on a number of specific molecules.
Author: McClure, William Submitted by: Martz, Eric. (Entry 65). Submitted on Aug 22, 2000. Last revised on Aug 22, 2000.
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Chime made easy to use :
Protein Explorer for Novices. (Martz, Eric)
Chime methods and tools :
How to Create New Chime Tutorials. (Martz, Eric)
Chime Square:
Cross-indexing terms: metabolism; glycolysis; gluconeogenesis; electron transport chain; oxidative stress; oxidative phosphorylation; nitrogenase; photosynthesis; dioxygen carriers; citric acid cycle; metalloproteins; nucleic acids; DNA; DNA-binding; transcription factors; leucine zippers; zinc fingers; repressors; activators.
"Chime Square" contains over 100 presentation emphasizing proteins involved in selected metabolic pathways, metalloproteins, and DNA-binding proteins. The user interface assumes familiarity with Chime mouse controls along with a background in protein and nucleic acid biochemistry. This site is intended for those interested in exploring the relationship between structure and function associated with proteins and nucleic acids commonly encountered in biochemistry courses.
Author: Niederhoffer, Eric Submitted by: the author. (Entry 40). Submitted on Jul 8, 2000. Last revised on Jun 12, 2001.
Chime: Great Sites:
Cross-indexing terms: organic chemistry sites; molecules, sources of, organic (PDB files); links to Chime sites.
One of the most extensive lists of annotated links to diverse Chime sites. Organic chemistry tutorials and sites are especially well represented here. Includes several sources of small "molecules" (atomic coordinate or PDB) files.
Author: MDL Information Systems, Inc. Submitted by: Martz, Eric. (Entry 9). Submitted on May 25, 2000.
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chloramphenicol acetyl transferase :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
Chlorophyll :
Molecule of the Month/University of Bristol. (May, Paul (editor))
cholera toxin :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
Cholesterol :
Molecules for Modern/Cell Biology. (McClure, William)
Cholesterol :
Isoprenoid Biosynthesis Pathway. (Warren, L. Van)
Cholesterol :
Lipid Bilayers and the Gramicidin Channel. (Martz, Eric; Herraez, Angel)
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chromophore :
GFP (Green Fluorescent Protein). (Driscoll, Timothy)
chromosome rearrangement :
Hin Recombinase (at The Online Macromolecular Museum). (Millard, Elizabeth; Downs, Aaron; Marcey, David)
chymotrypsin :
Chemical Bonds and Protein Structure (at The Online Macromolecular Museum). (Marcey, David)
cis-g-Irone :
Molecule of the Month/University of Bristol. (May, Paul (editor))
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Cisplatin :
Molecule of the Month/University of Bristol. (May, Paul (editor))
Citric acid cycle :
Images of TCA Cycle Intermediates. (McClure, William)
Citric acid cycle :
Chime Square. (Niederhoffer, Eric)
Classroom use of Chime :
Student Webpapers: The Structure-Function Relationships for the Enzymes in the Glycolytic and Lactate Fermentation Pathways. (Chem406 Class, Fall 1999, U Wisc-Eau Claire)
Clathrin :
The Lycoming College Macromolecular Modeling and Bioinformatics Page. (Newman, Jeff)
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cloning :
Restriction Enzymes: Eco RV. (Reichsman, Frieda)
colicin :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
collagen :
Biomodel. (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish)
collagen :
BioMolecular Explorer 3D: Resources for High School Biology. (Reichsman, Frieda; Eric Martz)
Collagen (1a89.pdb), a theoretical model of the triple helix :
Protein Structures List. (McClure, William)
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color-coded multiple sequence alignment :
AHo's Amazing Atlas of Antibody Structure. (Honegger, Annemarie)
comparison of 2 molecules :
MolUSc - Molecules pour un Usage Scholaire. (Pillot, Paul) (French)
complementarity-determining regions :
Antibody Recognition of Antigen (at The Online Macromolecular Museum). (Marcey, David)
complementarity-determining regions in antibody :
Antibody. (Martz, Eric)
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concanavalin a :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
Concanavalin A (2cna.pdb), an antiparallel β-barrel :
Protein Structures List. (McClure, William)
conformational change :
Hemoglobin I. (White, Brian)
conformational changes in G proteins :
G Proteins (Trimeric): Molecular On/Off Switches, at Biochemistry in 3D. (Reichsman, Frieda; Driscoll, Timothy)
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conformational changes in ras oncogene product :
Ras Oncogene Product. (Gorga, Frank)
conformational changes, morphs :
Morpher, Protein. (Martz, Eric)
conservation :
ConSurf Server for the Identification of Functional Regions in Proteins by Surface Mapping of Phylogenetic Information. (Glaser, Fabian; Ben-Tal, Nir; Pupko, Tal; Martz, Eric)
ConSurf Server for the Identification of Functional Regions in Proteins by Surface Mapping of Phylogenetic Information:
Cross-indexing terms: mutation; evolution; conservation; multiple sequence alignment coloring of a protein; hypervariable residues.
ConSurf identifies, in Chime (actually, in Protein Explorer) the most highly conserved residues, and the hypervariable residues, based on a multiple sequence alignment and phylogenetic tree. It works on any protein for which a 3D structure is available. ConSurf is completely automatic. All you have to provide is the PDB code for a 3D structure, and specify which chain to work on. Optionally, you can provide your own multiple sequence alignment. Image at left: enolase (4enl) -- click on it to go to the ConSurf Gallery.
Authors: Glaser, Fabian; Ben-Tal, Nir; Pupko, Tal; Martz, Eric. Submitted by: Martz, Eric. (Entry 135). Submitted on Jul 1, 2002. Last revised on Oct 9, 2002.
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Contact surfaces :
Protein Explorer, Advanced. (Martz, Eric; (MSA3D component coauthored by Paul Stothard))
coordination at metal site :
Rubisco: a first look at the mechanism. An experiment in molecular visualisation. (Nixon, John)
CopG :
Biomolecules at Kenyon College. (Students, Kenyon College; Site Director, Joan Slonczewski) (English; CopG auf Deutch)
copper :
Interactive Quercetin 2,3-Dioxygenase Presentation. (Pijning, T)
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copper proteins :
Redox Proteins. (Hansson, Orjan)
Course Home Page for "Computer Applications in Biotechnology":
Cross-indexing terms: NMR; amino acids; animated gifs; spermine; nucleotides; student-authored tutorials.
"Computer Applications in Biotechnology" is a project-based class in which students create interactive tutorials using RasMol and Chemscape Chime. There are many links to examples of student projects. For example, one class project involves illustrating NMR spectra of amino acids and nucleotides using interactive Chime models.
Author: Klevickis, Cindy Submitted by: the author. (Entry 50). Submitted on Jul 20, 2000.
cro repressor :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
Cro Repressor of Temperate Bacteriophages (at The Online Macromolecular Museum):
Cross-indexing terms: bacteriophage cro; bacteriophage repressor; operator DNA; transcription regulation; genetic switch.
Cro, a repressor protein of temperate bacteriophages (e.g. lambda, 434, P22), works in opposition to the phage's repressor to control the genetic switch that determines whether a lytic or lysogenic cycle will follow infection. This Chime-based exhibit explores the structure of cro.
Author: Marcey, David Submitted by: the author. (Entry 125). Submitted on Jul 24, 2001.
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cupin :
Interactive Quercetin 2,3-Dioxygenase Presentation. (Pijning, T)
curriculum resources for biochemistry :
. (Biochemistry and Molecular Biology, American Society of)
cyclamate :
Everything You Ever Wanted to Know about Sweeteners. (Walters, D. Eric)
cycloalkanes :
Web-Based Chemical Investigations. (Bragin, Victoria (Vicki))
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CYP101 :
Cytochrome P450 3D structures page. (Nelson, David)
CYP2C5 :
Cytochrome P450 3D structures page. (Nelson, David)
cytochrome bc1 :
Molecular Science Lab. (Oberholser, Karl)
cytochrome bc1 :
Animations on subjects of Structural and Metabolic Biochemistry. (Silva, Pedro)
cytochrome c oxidase :
Molecular Science Lab. (Oberholser, Karl)
cytochrome c oxidase :
Animations on subjects of Structural and Metabolic Biochemistry. (Silva, Pedro)
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Cytochrome P450 :
Cytochrome P450 3D structures page. (Nelson, David)
Cytochrome P450 3D structures page:
Cross-indexing terms: Cytochrome P450; P450cam; CYP2C5; CYP101; oxygen binding pocket; WXXXR motif; EXXR motif; PKG motif; PERF motif; C-helix; I-helix; K-helix; thiolate ligand.
This site provides a 3D structure primer on cytochrome P450. The initial page includes 37 images made as RasMol scripts and embedded in a Chime template for interactive viewing. These images start at the bare PDB output for P450 cam (CYP101) and move to more and more detail on P450 structure. This includes a tour of the conserved motifs in the more than 2500 P450 sequences known. Each motif is visited with the intent of understanding what the conserved residues are doing in the structure of the protein. This is rather like walking around in a big version of the molecule to see how it is put together. This approach frequently leads to charge pairs critical to the protein fold and sometimes to charge triads. Some images are from CYP2C5, a mammalian P450 with motifs absent in the bacterial P450s. The 3D pages are part of a larger Cytochrome P450 homepage, in operation since 1995 at this same URL. Page created Nov. 2002.
Author: Nelson, David Submitted by: the author. (Entry 144). Submitted on Nov 21, 2002. Last revised on Nov 22, 2002.
cytochromes :
Redox Proteins. (Hansson, Orjan)
cytokine :
Erythropoietin - EPO Receptor Complex (at The Online Macromolecular Museum). (Marcey, David)
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DALI :
XdomView: A Chime-based Graphical Tool for Protein Domain and Exon Position Visualization. (Gopalan, Vivek; Shoba Ranganathan; Tan Tin Wee)
databases on-line :
Protein Structure Analysis Using Internet Tools: A Tutorial Using Peroxidase. (Rojas, Nina Rosario L.; Quiambao, Paul Rosby M.)
deoxyhemoglobin :
Animations on subjects of Structural and Metabolic Biochemistry. (Silva, Pedro)
deoxyribonucleic acid, DNA, major groove, minor groove :
B-Form Deoxyribonucleic Acid (DNA). (Bruist, Michael)
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deoxyribose :
DNA Structure. (Reichsman, Frieda) (English, Italian)
Desmosterol :
Isoprenoid Biosynthesis Pathway. (Warren, L. Van)
dethiobiotin synthetase :
Magnesium Adenosine Triphosphate (MgATP) Binding to an Enzyme. (Bruist, Michael)
diabetes :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
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diffusion :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
Dihydrofolate reductase :
The Lycoming College Macromolecular Modeling and Bioinformatics Page. (Newman, Jeff)
dioxygen carriers :
Chime Square. (Niederhoffer, Eric)
dioxygenase :
Interactive Quercetin 2,3-Dioxygenase Presentation. (Pijning, T)
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diphtheria toxin :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
disease :
Sickle Cell Anemia: Understanding the Molecular Biology. (Sabo, John; Lynch, Jamie; Raineri, Deanna)
disulfide bond :
Molecules and Structures Homepage. (Gasser, Charles)
disulfide bonds in immunoglobulin :
Antibody. (Martz, Eric)
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DNA :
Molecule of the Month/University of Bristol. (May, Paul (editor))
DNA :
Chime Square. (Niederhoffer, Eric)
DNA :
Sickle Cell Anemia: Understanding the Molecular Biology. (Sabo, John; Lynch, Jamie; Raineri, Deanna)
DNA :
Biomodel. (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish)
DNA :
RecA Protein (at The Online Macromolecular Museum). (Heerssen, Heather; Downs, Aaron; Marcey, David)
DNA :
Biomolecular Structures. (Hansson, Orjan)
DNA :
Macromolecular Visualization Laboratory Exercise. (Kahn, Kalju)
DNA :
BioMolecular Explorer 3D: Resources for High School Biology. (Reichsman, Frieda; Eric Martz)
DNA & RNA :
Molecules for Modern/Cell Biology. (McClure, William)
DNA (1bna.pdb) :
Overviews of DNA & RNA Structure. (McClure, William)
DNA binding :
MutS DNA Repair Protein (at The Online Macromolecular Museum). (Stoffregen, Eric; Marcey, David)
DNA binding :
HIV-1 Integrase (at The Online Macromolecular Museum). (Walsh, Matthew; Marcey, David)
DNA binding :
Hin Recombinase (at The Online Macromolecular Museum). (Millard, Elizabeth; Downs, Aaron; Marcey, David)
DNA binding :
HhaI DNA Methyltransferase (at The Online Macromolecular Museum). (Douglass, Ben; Downs, Aaron; Marcey, David)
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DNA binding protein :
The E. coli trp Repressor Chime Movie. (Lawson, Cathy)
DNA binding protein :
The Zinc Finger: A Protein Domain that Binds Specific DNA Sequences. (Bruist, Michael)
DNA cleavage :
BamHI Restriction Endonuclease (at The Online Macromolecular Museum). (Silva, Nathan; Leslie, Kenneth; Marcey, David)
DNA Conformers (at The Online Macromolecular Museum):
Cross-indexing terms: DNA Structure; A-DNA; B-DNA; Z-DNA.
This Chime-based tutorial compares the essential structural features of A-, B-, and Z-DNA.
Author: Marcey, David Submitted by: the author. (Entry 142). Submitted on Oct 2, 2002.
DNA glycosylase :
The Lycoming College Macromolecular Modeling and Bioinformatics Page. (Newman, Jeff)
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DNA methylation :
MutS DNA Repair Protein (at The Online Macromolecular Museum). (Stoffregen, Eric; Marcey, David)
DNA methylation :
HhaI DNA Methyltransferase (at The Online Macromolecular Museum). (Douglass, Ben; Downs, Aaron; Marcey, David)
DNA methylation :
MutH (at The Online Macromolecular Museum). (Carney, Jessica; Silva, Nathan; Marcey, David)
DNA modification :
HhaI DNA Methyltransferase (at The Online Macromolecular Museum). (Douglass, Ben; Downs, Aaron; Marcey, David)
DNA polymerase :
DNA Polymerase III-Beta Subunit (at The Online Macromolecular Museum). (Marcey, David)
DNA polymerase :
DNA Polymerase I from Thermus aquaticus. (Bruist, Michael)
DNA Polymerase Beta (at The Online Macromolecular Museum):
Cross-indexing terms: polB; polymerase, DNA.
DNA polymerase Beta (pol B) is a eukaryotic DNA polymerase studied most extensively in vertebrate systems. Like other DNA polymerases, pol B is responsible for adding new nucleotides to a growing chain by catalyzing a nucleotidyl transfer reaction. This Chime-based exhibit explores structural aspects of Pol B catalysis, DNA binding, processivity, and fidelity.
Authors: Fries, David; Marcey, David. Submitted by: Marcey, David. (Entry 110). Submitted on Jun 17, 2001.
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DNA Polymerase I from Thermus aquaticus:
Cross-indexing terms: DNA polymerase; primer; template; polymerization mechanism; exonuclease; DNA substrate; DNA polymerase tutorial; SN1 reaction; lesson plan.
This chime window presents students with DNA polymerase in the act of adding a nucleotide to a primer. Both the polymerization domain and 3' to 5' exonuclease are depicted. The template and primer strands along with the incoming nucleotide can be viewed in various modes. There is a zoom into the active site enabling one to clearly see how an SN1 reaction will add the nucleotide to the primer DNA strand. The window functions as a tutorial in which several questions are posed, with answers available with a click. The coordinates have been modified so that actual substrates rather than inhibitors are seen on the enzyme.
Author: Bruist, Michael Submitted by: the author. (Entry 136). Submitted on Sep 10, 2002.
DNA Polymerase III-Beta Subunit (at The Online Macromolecular Museum):
Cross-indexing terms: DNA polymerase; Sliding DNA clamp; processivity subunit.
The beta subunit of DNA pol III (E. coli)provides for the remarkable processivity of the holoenzyme during replication. The subunit is a ring-shaped clamp that embraces DNA in a central 35 angstrom hole and tethers the remainder of pol III to the template. This Chime-based exhibit explores the structure and function of the polIII beta subunit.
Author: Marcey, David Submitted by: the author. (Entry 107). Submitted on Jun 17, 2001.
DNA Polymerase of Bacteriophage T7 (at The Online Macromolecular Museum):
Cross-indexing terms: Metal ion-induced catalysis.
The bacteriophage T7 DNA replication complex is a good model system for the study of the mechanism of DNA synthesis because it consists of relatively few proteins. This Chime-based exhibit focuses on how processivity is maintained during DNA synthesis, on how metal cations are involved in nucleotide addition, and on how T7 DNA polymerase recognizes specific nucleotides.
Authors: Ward, Michael; Marcey, David. Submitted by: Marcey, David. (Entry 109). Submitted on Jun 17, 2001.
DNA polymerase tutorial :
DNA Polymerase I from Thermus aquaticus. (Bruist, Michael)
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DNA polymerases :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
DNA quizzer:
Cross-indexing terms: DNA sequence and quizzer; quizzer, DNA; lab exercise; lesson plan.
A lab exercise in DNA structure. Students select a short DNA sequence by number & must deterine its nucleotide sequence.
Author: White, Brian Submitted by: the author. (Entry 81). Submitted on Nov 10, 2000.
DNA recombination :
RecA Protein (at The Online Macromolecular Museum). (Heerssen, Heather; Downs, Aaron; Marcey, David)
DNA recombination :
RecA Protein (at The Online Macromolecular Museum). (Heerssen, Heather; Downs, Aaron; Marcey, David)
DNA recombination :
HIV-1 Integrase (at The Online Macromolecular Museum). (Walsh, Matthew; Marcey, David)
DNA recombination :
Hin Recombinase (at The Online Macromolecular Museum). (Millard, Elizabeth; Downs, Aaron; Marcey, David)
DNA repair :
MutS DNA Repair Protein (at The Online Macromolecular Museum). (Stoffregen, Eric; Marcey, David)
DNA repair :
MutH (at The Online Macromolecular Museum). (Carney, Jessica; Silva, Nathan; Marcey, David)
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DNA sequence and quizzer :
DNA quizzer. (White, Brian)
DNA Structure: (English, German, Portuguese, Spanish )
Cross-indexing terms: GC base pair; AT base pair; hydrogen bonding, Watson-Crick; Watson-Crick base pairing and hydrogen bonding; double helix, DNA.
At : Chime images of a 17-base-pair DNA double helix. This is not a self-contained tutorial, but rather a supplement to a text or class on DNA structure. Buttons which highlight features of the DNA may be pressed in any order, and their actions depend on which buttons were pressed earler. For example, [Bases] followed by [Spacefill] spacefills all the base pairs (but not the backbone), whereas [GC] followed by [Spacefill] spacefills the single GC base pair. Four pages emphasize (1) base pairs and hydrogen bonding, (2) the code, (3) strands and helical backbone, and (4) ends and antiparallelism. A simple animation of base-by-base replication is included. The nonlinear/random button interface is unique among Chime presentations on the web. Downloadable for off-line use, local installation or modification. New version July 2002 is compatible with Windows Internet Explorer, and has other enhancements.
Also available in German, Portuguese, and Spanish.
Author: Martz, Eric Submitted by: the author. (Entry 12). Submitted on May 28, 2000. Last revised on Oct 1, 2004.
DNA Structure :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
DNA Structure: (English, Italian )
Cross-indexing terms: nucleic acids; double helix; base pairs; deoxyribose.
Chime-based tutorial including fundamentals of backbone structure, basepairing and helix stabilization. Detailed look at sugar and base configuration/numbering schemes, and strand direction. References to figures in Stryer's Biochemistry, 4th edition. Implementation includes text, movies, and help. Available in Italian courtesy of Giuseppe Striccoli.
Author: Reichsman, Frieda Submitted by: the author. (Entry 34). Submitted on Jun 3, 2000. Last revised on Feb 13, 2002.
DNA Structure :
DNA Conformers (at The Online Macromolecular Museum). (Marcey, David)
DNA Structure :
DNA Structure (at The Online Macromolecular Museum). (Marcey, David)
DNA Structure (at The Online Macromolecular Museum):
Cross-indexing terms: B-DNA; DNA structure; major groove; minor groove; nucleotide; phosphodiester linkage; antiparallel strands.
This Chime-based exhibit explores the structures of the B-DNA polymer and B-form double helix.
Author: Marcey, David Submitted by: the author. (Entry 143). Submitted on Oct 2, 2002.
DNA Structure (with Jmol):
Cross-indexing terms: GC base pair; AT base pair; hydrogen bonding, Watson-Crick; Watson-Crick base pairing and hydrogen bonding; double helix, DNA; Jmol.
Adaptation of the existing "DNA Structure" by Eric Martz, using Jmol instead of Chime. Compatible with most modern browsers and operating systems (including MacOSX and Linux). Needs Java installed. Also available in Spanish.
Authors: Herraez, Angel; Martz, Eric. Submitted by: the author. (Entry 162). Submitted on Mar 14, 2005.
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DNA substrate :
DNA Polymerase I from Thermus aquaticus. (Bruist, Michael)
DNA supercoiling :
DNA Topoisomerase I (at The Online Macromolecular Museum). (Kysela, David; Marcey, David)
DNA Topoisomerase I (at The Online Macromolecular Museum):
Cross-indexing terms: topoisomerase, type I; DNA supercoiling; DNA unwinding.
E. coli DNA Topoisomerase I is responsible for the relaxation of negative supercoils in the bacterial chromosome. Topoisomerase I has also been implicated in knotting and unknotting DNA and in linking complementary rings of single-stranded DNA into double-stranded rings. The focus of this Chime-based exhibit is the structure-function relationships of the 67K, N-terminal fragment of Topoisomerase I.
Authors: Kysela, David; Marcey, David. Submitted by: Marcey, David. (Entry 102). Submitted on Jun 17, 2001.
DNA unwinding :
DNA Topoisomerase I (at The Online Macromolecular Museum). (Kysela, David; Marcey, David)
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DNA, A, B, and Z forms :
Nucleic Acid Structure Tutorials. (Nolan, Jim)
DNA, single stranded :
RecA Protein (at The Online Macromolecular Museum). (Heerssen, Heather; Downs, Aaron; Marcey, David)
DNA-binding :
Chime Square. (Niederhoffer, Eric)
DNA-binding protein :
BamHI Restriction Endonuclease (at The Online Macromolecular Museum). (Silva, Nathan; Leslie, Kenneth; Marcey, David)
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DNA-protein interactions :
Nucleic Acid Structure Tutorials. (Nolan, Jim)
domain :
XdomView: A Chime-based Graphical Tool for Protein Domain and Exon Position Visualization. (Gopalan, Vivek; Shoba Ranganathan; Tan Tin Wee)
Domain IV RNA Structure (1cq5.pdb). :
Signal Recognition Particle. (McClure, William)
domains :
AHo's Amazing Atlas of Antibody Structure. (Honegger, Annemarie)
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domains, protein :
Protein Architecture at Biochemistry in 3D. (Driscoll, Timothy; Reichsman, Frieda)
double helix :
DNA Structure. (Reichsman, Frieda) (English, Italian)
double helix, DNA :
DNA Structure. (Martz, Eric) (English, German, Portuguese, Spanish)
double helix, DNA :
DNA Structure (with Jmol). (Herraez, Angel; Martz, Eric)
drug discovery :
The Rational Basis of Drug Design. (Walters, D. Eric)
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Dystrophin :
The Lycoming College Macromolecular Modeling and Bioinformatics Page. (Newman, Jeff)
E. coli Ffh protein: the protein subunit without RNA (2ffh.pdb) :
Signal Recognition Particle. (McClure, William)
E. coli Glycerol Channel (1fx8.pdb, 1ldi.pdb) :
Membrane Channel & Pump Structures. (McClure, William)
E. coli Porins: OMPF and Maltoporin (LamB) :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
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EcClC Chloride Channel (1ots.pdb, 1otu.pdb) :
Membrane Channel & Pump Structures. (McClure, William)
EcoRI :
Protein/DNA interactions. (Gibson, Andrew; Sims, P. F. G.)
EcoRI Res. Endonuclease :
Structures for Molecular Biology. (McClure, William)
EF-hand, morph :
Morpher, Protein. (Martz, Eric)
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EF-Tu :
Biomodel. (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish)
EF-Tu, tRNAPhe, and GTP :
Structures for Molecular Biology. (McClure, William)
electron transport chain :
Chime Square. (Niederhoffer, Eric)
electron transport chain :
Animations on subjects of Structural and Metabolic Biochemistry. (Silva, Pedro)
Elements :
Molecules for Modern/Cell Biology. (McClure, William)
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elements, periodic table of :
3D Periodic Table of Radii. (Wherland, Scot)
Enantiomers of glyceraldehyde :
Molecules for Modern/Cell Biology. (McClure, William)
endonuclease :
Restriction Enzymes: Eco RV. (Reichsman, Frieda)
endonuclease MutH :
MutH (at The Online Macromolecular Museum). (Carney, Jessica; Silva, Nathan; Marcey, David)
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Engrailed :
Molecules and Structures Homepage. (Gasser, Charles)
enolase :
The Glycolytic Cycle. (Warren, L. Van)
enzyme active site :
Carboxypeptidase A - Three Exercises with Chime. (Morgan, Eleanor; Helmerhorst, Erik)
enzyme kinetics :
Rubisco: a first look at the mechanism. An experiment in molecular visualisation. (Nixon, John)
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enzyme mechanism :
The Large Ribosomal Subunit: a structure/function tutorial. (Sontum, Stephen; Lesko, Zack)
enzyme-substrate complex :
Alkaline phosphatase. (White, Brian)
epitope structure, lysozyme bound to antibody :
Antibody. (Martz, Eric)
epitopes, T-cell :
Major Histocompatibility Complex. (Martz, Eric)
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EPO :
Erythropoietin - EPO Receptor Complex (at The Online Macromolecular Museum). (Marcey, David)
Erythropoietin :
Erythropoietin - EPO Receptor Complex (at The Online Macromolecular Museum). (Marcey, David)
Erythropoietin - EPO Receptor Complex (at The Online Macromolecular Museum):
Cross-indexing terms: EPO; Erythropoietin; receptor binding; cytokine.
Erythropoietin (EPO), a cytokine hormone, is responsible for the regulation of red blood cell production. EPO is a glycoprotein produced primarily in the the kidney. Secreted EPO (165 amino acids) binds to EPO receptors on the surface of bone marrow erythroid precursors, resulting in their rapid replication and maturation to functional red blood cells. This Chime-based exhibit explores EPO and EPO Receptor structure and binding.
Author: Marcey, David Submitted by: the author. (Entry 130). Submitted on Feb 22, 2002.
Estrogen Receptor Structures & Function:
Cross-indexing terms: nuclear hormone receptor; transcription activation.
An "Overview" provides a brief introduction to the estrogen receptor (ER) and its functions, including literature citations and WWW links. The Chime pages show ERα and ERβ as dimers and focus on the ligand specificity and conformational changes that accompany agonist or antagonist binding to the ligand-binding domain (LBD). The LBD complexes include the agonists: estradiol, diethlystilbestrol, and genistein; the antagonists shown are: raloxifene and tamoxifen. Differences between the ERα and ERβ complexes are shown separately and as superimposed (aligned) models. The ER DNA-binding domain (DBD) complex with an ERE is also shown. Linked pages show small molecule models of the above ligands and several other estrogens and steroids.
PDB ID codes: 1ERE, 1ERR, 3ERD, 3ERT, 1A52, 1QKM, 1QKN, 1HCQ.
Authors: McClure, Will; Saha, Suparna. Submitted by: the author. (Entry 95). Submitted on Jun 6, 2001.
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Estructura de Macromoleculas: (Spanish )
Cross-indexing terms: General protein structure; General DNA structure.
CHIME-based visualization of small biomolecules and elements corresponding to the different structural levels of proteins and DNA (primary, secondary, supersecondary, tertiary and quaternary structures). RASMOL scripts translated to Spanish (from the RASMOL home pageand UMASS resources page) Links related to biological macromolecular structure. This page is thoroughly used for academic teaching.
[pic]
Visualizacion en CHIME de biomoleculas pequenas y de elementos correspondientes a diferentes niveles estructurales de proteinas (primario, secundario, supersecundario,terciario, cuaternario) y de DNA. "Scripts" de Rasmol a partir de la "home page" deRASMOL y la pagina de recursos de UMASS traducidos al castellano. Enlaces a bases de datos de estructura de macromoleculas biologicas. Esta pagina es muy adecuada para clases academicas.
Author: Sanz, Jesus M. Submitted by: the author. (Entry 67). Submitted on Sep 5, 2000. Last revised on Jul 11, 2002.
Eukaryotic DNA Polymerase Beta :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
Everything You Ever Wanted to Know about Sweeteners:
Cross-indexing terms: sweetener; acesulfame; aspartame; cyclamate; saccharin; sucralose.
Contains information about commonly used high potency sweeteners: acesulfame, aspartame, cyclamate, saccharin, and sucralose. Included for each sweetener are molecular formula, molecular weight, chemical structure, chemical and commercial names, Chime structures, stories about the discovery of sweeteners, and concentration-vs.-response data.
Author: Walters, D. Eric Submitted by: the author. (Entry 72). Submitted on Nov 6, 2000.
evolution :
ConSurf Server for the Identification of Functional Regions in Proteins by Surface Mapping of Phylogenetic Information. (Glaser, Fabian; Ben-Tal, Nir; Pupko, Tal; Martz, Eric)
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ExInt :
XdomView: A Chime-based Graphical Tool for Protein Domain and Exon Position Visualization. (Gopalan, Vivek; Shoba Ranganathan; Tan Tin Wee)
exon :
XdomView: A Chime-based Graphical Tool for Protein Domain and Exon Position Visualization. (Gopalan, Vivek; Shoba Ranganathan; Tan Tin Wee)
exons :
Sickle Cell Anemia: Understanding the Molecular Biology. (Sabo, John; Lynch, Jamie; Raineri, Deanna)
exonuclease :
DNA Polymerase I from Thermus aquaticus. (Bruist, Michael)
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Explore the c-Src tyrosine kinase:
Cross-indexing terms: tyrosine kinase; kinase, tyrosine; src-family.
A chime-based, tutorial page of the structure of the tyrosine kinase c-Src. Buttons allow the user to selectively highlight important domains and residues critical for regulation of Src and its family members. A link in the page takes you to more information about c-Src, its properties, and regulation.
Authors: Engen, John R; Superti-Furga, Giulio. Submitted by: the author. (Entry 46). Submitted on Jul 17, 2000.
Explorer, Protein :
Protein Explorer for Novices. (Martz, Eric)
Exploring Glyceraldehyde-3-phosphate dehydrogenase:
Cross-indexing terms: glyceraldehyde-3-phosphate dehydrogenase; NAD+ binding; glyceraldehyde-phosphate binding; quaternary structure.
This page explores the heirarchy of protein structure. Glyceraldehyde-3-phosphate dehydrogenase is a homotetramer. The arrangement of the four subunits is observed. An animation goes from the space-filling tetramer to a single subunit, which is then converted to a ribbon cartoon. It is seen that each domain binds one substrate. The secondary features that comprise the NAD+ binding domain are presented. These can be isolated or seen in contect of the full domain. Side chains can be toggled on and off.
Author: Bruist, Michael Submitted by: the author. (Entry 138). Submitted on Sep 10, 2002.
extracellular matrix :
Fibronectin (at The Online Macromolecular Museum). (Ward, Michael; Marcey, David)
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Extracellular Matrix Components :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
EXXR motif :
Cytochrome P450 3D structures page. (Nelson, David)
factor II :
Structural Biochemistry of Blood Coagulation. (Walters, D. Eric)
factor III :
Structural Biochemistry of Blood Coagulation. (Walters, D. Eric)
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factor IX :
Structural Biochemistry of Blood Coagulation. (Walters, D. Eric)
factor VII :
Structural Biochemistry of Blood Coagulation. (Walters, D. Eric)
factor XIII :
Structural Biochemistry of Blood Coagulation. (Walters, D. Eric)
Farnesyl pyrophosphate :
Isoprenoid Biosynthesis Pathway. (Warren, L. Van)
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Fats: Glycerol & Fatty Acids :
Molecules for Modern/Cell Biology. (McClure, William)
Ferritin :
Molecule of the Month/University of Bristol. (May, Paul (editor))
fibrin :
Structural Biochemistry of Blood Coagulation. (Walters, D. Eric)
Fibronectin :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
Fibronectin :
The Lycoming College Macromolecular Modeling and Bioinformatics Page. (Newman, Jeff)
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Fibronectin (at The Online Macromolecular Museum):
Cross-indexing terms: extracellular matrix; integrin; RGD.
Fibronectin (FN) is involved in many cellular processes, including tissue repair, embryogenesis, blood clotting, and cell migration/adhesion. FN exists in two main forms: 1) as an insoluble glycoprotein dimer that serves as a linker in the extracellular matrix, and; 2) as a soluble disulphide linked dimer found in the plasma. This Chime-based exhibit exlores the structure-function relationships of FN.
Authors: Ward, Michael; Marcey, David. Submitted by: Marcey, David. (Entry 98). Submitted on Jun 17, 2001.
fibrous proteins :
Molecular Science Lab. (Oberholser, Karl)
Finasteride :
Molecule of the Month/University of Bristol. (May, Paul (editor))
Flagellar Hook, Bacterial -- A Molecular Universal Joint:
Cross-indexing terms: hook, flagellar; universal joint, molecular: flagellar hook.
Animations of the rotation of the bacterial flagellar hook, based on a crystal structure of the monomer, 121 copies of which were assembled into a cryo-EM structure of the hook, and rotated by molecular dynamics simulation. Based on work by Samatey et al. in the groups of DeRosier and Namba, published in Nature 431:1062, October 2004.
Author: Martz, Eric Submitted by: the author. (Entry 161). Submitted on Dec 20, 2004. Last revised on Dec 20, 2004.
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flu virus :
Viral Antigens (at The Online Macromolecular Museum). (Mazur, Eric; Marcey, David)
fluorescence :
GFP (Green Fluorescent Protein). (Driscoll, Timothy)
Formaldehyde :
Molecule of the Month/University of Bristol. (May, Paul (editor))
Fos :
Molecules and Structures Homepage. (Gasser, Charles)
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fosmidomycin :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
Frankincense :
Molecule of the Month/University of Bristol. (May, Paul (editor))
French :
MolUSc - Molecules pour un Usage Scholaire. (Pillot, Paul) (French)
FSSP :
XdomView: A Chime-based Graphical Tool for Protein Domain and Exon Position Visualization. (Gopalan, Vivek; Shoba Ranganathan; Tan Tin Wee)
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FtsZ, a prokaryotic cell-division protein and tubulin homologue.:
Cross-indexing terms: tubulin; Presentation in Protein Explorer (PIPE - prototype); GTP-binding protein FtsZ.
A detailed tour of FtsZ structure, including a sequence alignment, fluorescence a time-lapse movie of the protein in dividing cells, with over 50 views in Chime. The GTP-binding motif and structural alignment of FtsZ and tubulin are featured. This presentation is a prototype within Protein Explorer 1.0. This means you can use the full capabilities of Protein Explorer to manipulate any view in the presentation.
Author: McCool, Gabriel J. Submitted by: Martz, Eric. (Entry 8). Submitted on May 25, 2000.
Functional Groups :
Molecules for Modern/Cell Biology. (McClure, William)
G protein, low molecular weight :
Ras Oncogene Product. (Gorga, Frank)
G proteins :
G Proteins (Trimeric): Molecular On/Off Switches, at Biochemistry in 3D. (Reichsman, Frieda; Driscoll, Timothy)
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G Proteins (Trimeric): Molecular On/Off Switches, at Biochemistry in 3D:
Cross-indexing terms: Lehninger's Principles of Biochemistry; G proteins; GTP/GDP binding site and induced conformational changes; conformational changes in G proteins.
Chime-based tutorial on trimeric G proteins including 3 switch regions near the GTP/GDP-binding site, detailed look at the conformational changes upon GTP hydrolysis or GDP/GTP exchange, dissociation of the alpha chain from the beta/gamma chains and its control by switch regions. References to figures in Lehninger's Principles of Biochemistry (Lehninger, Nelson & Cox), 3rd edition. Implementation includes pop-up detail boxes, movies, color keys, extensive help, busy/idle status indicators, and a powerful interface for self-directed exploration of the tutorial images.
Authors: Reichsman, Frieda; Driscoll, Timothy. Submitted by: Driscoll, Timothy. (Entry 2). Submitted on May 24, 2000. Last revised on Jun 15, 2000.
G-protein Beta and Gamma subunits :
The Lycoming College Macromolecular Modeling and Bioinformatics Page. (Newman, Jeff)
Gal4 :
Molecules and Structures Homepage. (Gasser, Charles)
Garrett & Grisham Interactive Biochemistry:
Cross-indexing terms: albumin; secondary structure; myoglobin; major histocompatibility class I; nucleic acids.
The support site for Garrett & Grisham's Biochemistry text, including Chime-based tutorials on the topics listed above.
Authors: Garrett, R. H.; Grisham, C. M.. Submitted by: Martz, Eric. (Entry 129). Submitted on Jan 18, 2002.
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Garrett and Grisham Interactive Biochemistry Structure Tutorials:
Cross-indexing terms: nucleic acids; albumin, serum; myoglobin; MHC class I; secondary structure.
These structure tutorials support the Garrett and Grisham textbook, and require the Chime plug-in. Students can learn how to use Chime, and see tutorials on nucleic acids, serum albumin, myoglobin, the class I major histocompatibility complex (MHC I), and the alpha-helix.
Author: Caras, James Submitted by: the author. (Entry 83). Submitted on Dec 4, 2000.
GC base pair :
DNA Structure. (Martz, Eric) (English, German, Portuguese, Spanish)
GC base pair :
DNA Structure (with Jmol). (Herraez, Angel; Martz, Eric)
GCN4 :
Molecules and Structures Homepage. (Gasser, Charles)
gene :
XdomView: A Chime-based Graphical Tool for Protein Domain and Exon Position Visualization. (Gopalan, Vivek; Shoba Ranganathan; Tan Tin Wee)
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gene evolution :
XdomView: A Chime-based Graphical Tool for Protein Domain and Exon Position Visualization. (Gopalan, Vivek; Shoba Ranganathan; Tan Tin Wee)
gene expression :
Hin Recombinase (at The Online Macromolecular Museum). (Millard, Elizabeth; Downs, Aaron; Marcey, David)
gene regulation in bacteria :
Lac Repressor: Biochemistry in 3D. (Driscoll, Timothy)
General DNA structure :
Estructura de Macromoleculas. (Sanz, Jesus M.) (Spanish)
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General protein structure :
Estructura de Macromoleculas. (Sanz, Jesus M.) (Spanish)
genetic engineering :
Rubisco: a first look at the mechanism. An experiment in molecular visualisation. (Nixon, John)
genetic engineering :
Restriction Enzymes: Eco RV. (Reichsman, Frieda)
genetic switch :
Cro Repressor of Temperate Bacteriophages (at The Online Macromolecular Museum). (Marcey, David)
Geranyl pyrophosphate :
Isoprenoid Biosynthesis Pathway. (Warren, L. Van)
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GFP :
GFP (Green Fluorescent Protein). (Driscoll, Timothy)
GFP (Green Fluorescent Protein):
Cross-indexing terms: GFP; Aequoria victoria; beta barrel; fluorescence; chromophore; green fluorescent protein.
structural biology and reaction chemistry of the green fluorescent protein (GFP). uses Chime, gifs, and text in combination. supports use of Chime 1.x or higher. originally designed as a lecture aid, but can be used as a self-guided tutorial as well.
Author: Driscoll, Timothy Submitted by: the author. (Entry 145). Submitted on Dec 3, 2002.
globular proteins :
Molecular Science Lab. (Oberholser, Karl)
Glucocorticoid receptor :
Molecules and Structures Homepage. (Gasser, Charles)
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gluconeogenesis :
Chime Square. (Niederhoffer, Eric)
gluconeogenesis :
Student Webpapers: The Structure-Function Relationships for the Enzymes in the Glycolytic and Lactate Fermentation Pathways. (Chem406 Class, Fall 1999, U Wisc-Eau Claire)
glucose :
The Glycolytic Cycle. (Warren, L. Van)
glutamate receptor :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
glyceraldehyde-3-phosphate :
The Glycolytic Cycle. (Warren, L. Van)
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glyceraldehyde-3-phosphate dehydrogenase :
Exploring Glyceraldehyde-3-phosphate dehydrogenase. (Bruist, Michael)
glyceraldehyde-phosphate binding :
Exploring Glyceraldehyde-3-phosphate dehydrogenase. (Bruist, Michael)
glycolysis :
Images of Glycolysis Intermediates. (McClure, William)
glycolysis :
Chime Square. (Niederhoffer, Eric)
glycolysis :
Student Webpapers: The Structure-Function Relationships for the Enzymes in the Glycolytic and Lactate Fermentation Pathways. (Chem406 Class, Fall 1999, U Wisc-Eau Claire)
glycosylation :
Interactive Quercetin 2,3-Dioxygenase Presentation. (Pijning, T)
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glycosylation of antibody, N-linked :
Antibody. (Martz, Eric)
gramicidin channel :
Biomodel. (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish)
gramicidin channel in lipid bilayer :
Lipid Bilayers and the Gramicidin Channel. (Martz, Eric; Herraez, Angel)
green fluorescent protein :
GFP (Green Fluorescent Protein). (Driscoll, Timothy)
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GTP-binding protein FtsZ :
FtsZ, a prokaryotic cell-division protein and tubulin homologue. (McCool, Gabriel J.)
GTP/GDP binding site and induced conformational changes :
G Proteins (Trimeric): Molecular On/Off Switches, at Biochemistry in 3D. (Reichsman, Frieda; Driscoll, Timothy)
guanine nucleotide binding protein :
Ras Oncogene Product. (Gorga, Frank)
H-2 (mouse MHC) :
Major Histocompatibility Complex. (Martz, Eric)
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H2O cluster :
Molecules for Modern/Cell Biology. (McClure, William)
Hammerhead Ribozyme:
Cross-indexing terms: RNA; RNA enzyme; stem-loop; nucleophilic substitution; ribozyme.
This Chime tutorial includes basic aspects of RNA secondary structure, an SN2 reaction animation, a close look at catalysis, ribozyme reaction intermediates, and an animation of ground, intermediate, and product structures. Smooth transitions between views show their relationships clearly. The interface is easy to use for students and novices, but advanced users can modify the images with menus, or enter Chime commands.
Author: Reichsman, Frieda Submitted by: the author. (Entry 94). Submitted on Jun 5, 2001. Last revised on Jun 6, 2001.
helix-loop-helix :
Biomodel. (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish)
helix-turn-helix :
Biomodel. (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish)
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hemagglutinin, influenza :
Viral Antigens (at The Online Macromolecular Museum). (Mazur, Eric; Marcey, David)
Hemoglobin:
Cross-indexing terms: sickle hemoglobin.
At : A tutorial on hemoglobin in Chime including an introduction to stick, ball and stick, spacefill renderings, peptides and backbones, basic hemoglobin tetramer structure, heme, iron, histidine and oxygen binding to iron, secondary structure, zoom to one alpha helix and its hydrogen bonds, amphipathicity of helices, hydrophobic interior and polar surface of each monomer, sickle hemoglobin, its mutation and how that causes polymerization. Buttons can be pushed in any order yet always give the same images. Font size can be dymanically changed for large audiences. The utilities menu enables recentering, atom identification, measuring distances, and changing background color from black to white for printing. Downloadable for off-line use, local installation or modification.
Author: Martz, Eric Submitted by: the author. (Entry 13). Submitted on May 28, 2000. Last revised on Oct 1, 2004.
Hemoglobin :
Molecules for Modern/Cell Biology. (McClure, William)
Hemoglobin :
Oxygen Binding Proteins: Myoglobin and Hemoglobin. (Reichsman, Frieda; Driscoll, Timothy)
Hemoglobin :
Introduction to Protein Structure, Part I. (Bragin, Victoria (Vicki))
Hemoglobin :
Hemoglobin-S Polymerization Binding Site. (Howard, Vince)
Hemoglobin :
Sickle Cell Anemia: Understanding the Molecular Biology. (Sabo, John; Lynch, Jamie; Raineri, Deanna)
Hemoglobin :
Hemoglobin I. (White, Brian)
Hemoglobin :
Hemoglobin II. (White, Brian)
Hemoglobin :
Biomolecules at Kenyon College. (Students, Kenyon College; Site Director, Joan Slonczewski) (English; CopG auf Deutch)
Hemoglobin :
Biomodel. (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish)
Hemoglobin :
Molecular Science Lab. (Oberholser, Karl)
Hemoglobin :
BioMolecular Explorer 3D: Resources for High School Biology. (Reichsman, Frieda; Eric Martz)
Hemoglobin (oxy) (1hho.pdb), the red blood cell O2 carrier :
Protein Structures List. (McClure, William)
Hemoglobin I:
Cross-indexing terms: hemoglobin; side-chain interactions; conformational change.
A lecture-oriented chime 'slide show' about hemoglobin. Buttons show particular views (these must usually be played in order) and a caption appears in the lowest frame. This one shows hemoglobin - you can switch from deoxy to oxy & back in both spacefill & backbone views. You can alse see the 4 chains & heme. It then turns to b-globin & shows secondary structure as well as examples of an ionic bond, a hydrogen bond, and a hydrophobic interaction.
Author: White, Brian Submitted by: the author. (Entry 77). Submitted on Nov 10, 2000.
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Hemoglobin II:
Cross-indexing terms: hemoglobin; sickle-cell anemia; mutant proteins.
A lecture-oriented chime 'slide show' about hemoglobin. Buttons show particular views (these must usually be played in order) and a caption appears in the lowest frame. This one shows two mutants of hemoglobin & their effects:
• hemoglobin christchurch, which results in hemolytic anemia
• sickle-cell hemoglobin with the essential residues highlighted
Author: White, Brian Submitted by: the author. (Entry 78). Submitted on Nov 10, 2000.
Hemoglobin(deoxy) (1b86.pdb), with bound 2,3-bisphosphoglycerate (BPG) :
Protein Structures List. (McClure, William)
Hemoglobin-S Polymerization Binding Site:
Cross-indexing terms: hemoglobin; sickle cell anemia, point mutation; high school audience.
This is a draft demo of the hemoglobin-S polymerization binding site that results in sickle cell anemia due to a point mutation. The demo hi-lites the different hemoglobin chains, the heme groups within them, the point mutation, and the hydrophobic pocket in separate hemoglobin tetramers that bind to it such that polymerization occurs. The intended audience is high school advanced biology students.
Author: Howard, Vince Submitted by: the author. (Entry 64). Submitted on Aug 20, 2000.
hemolysin :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
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Hemolysin (7ahl.pdb), a heptameric channel-forming toxin :
Protein Structures List. (McClure, William)
herbicide :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
hexokinase :
The Glycolytic Cycle. (Warren, L. Van)
HhaI DNA Methylase :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
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HhaI DNA Methyltransferase (at The Online Macromolecular Museum):
Cross-indexing terms: DNA methylation; methyltransferases; DNA binding; DNA modification.
Methyltransferases are employed in restriction-modification and mismatch repair systems in prokaryotes, and have been implicated in many molecular processes in eukaryotes including regulation of gene expression, genomic imprinting, DNA repair, mutagenesis, and chromatin organization. HhaI DNA methyltransferase is a prokaryotic m5c-methyltransferase that recognizes the 5'-GCGC-3' sequence in double stranded DNA and methylates the first cysteine of the recognition sequence. This Chime-based exhibit explores the structure-function relationships of HhaI.
Authors: Douglass, Ben; Downs, Aaron; Marcey, David. Submitted by: Marcey, David. (Entry 106). Submitted on Jun 17, 2001.
HhaI Res. Methylase :
Structures for Molecular Biology. (McClure, William)
high school :
BioMolecular Explorer 3D: Resources for High School Biology. (Reichsman, Frieda; Eric Martz)
high school audience :
Hemoglobin-S Polymerization Binding Site. (Howard, Vince)
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high school biology :
BioMolecular Explorer 3D: Resources for High School Biology. (Reichsman, Frieda; Eric Martz)
Highlights of biochemistry: molecular structures made visible.: (English or German )
Cross-indexing terms: antibiotics; chloramphenicol acetyl transferase; concanavalin a; integration host factor; luciferase; lysozyme; nitrite reductase; proteasome; ribulose-1,5-bisphosphate carboxylase; rubisco; tobacco mosaic virus; TATA box binding protein; diphtheria toxin; hemolysin; cholera toxin; colicin; transport; porin; diffusion; ion channel; diabetes; jasmonic acid; hyperforin; Saint John's wort; sildenafil; fosmidomycin; malaria; toxoplasmosis; herbicide; IPA; Alzheimer's; bacterial photosynthesis; light harvesting complex; photosynthetic reaction center; Johanniskraut; glutamate receptor; actinomycin; archaeal rhodopsins; hydroxylamine oxidoreductase.
Interactive Chime scripts on selected topics of biochemistry - enzyme structures with special features up to reaction pathways.
Biochemie zum Ansehen: molekulare Strukturen vom Atom zum Makromolekuel:Interaktive Chime Skripte zu biochemischen Themen - von Enzymstrukturen mit Besonderheiten zu Reaktionswegen.
Author: Bergmann, Rolf Submitted by: the author. (Entry 52). Submitted on Jul 24, 2000. Last revised on Oct 20, 2001.
Hin Recombinase :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
Hin Recombinase (at The Online Macromolecular Museum):
Cross-indexing terms: DNA recombination; DNA binding; chromosome rearrangement; recombinase; gene expression.
Hin recombinase catalyzes a site-specific DNA inversion in the Salmonella chromosome. The recombination event regulates the alternate expression of two flagellin genes, H2 and H1. This Chime-based exhibit explores the structure-function relationships of the recombinase.
Authors: Millard, Elizabeth; Downs, Aaron; Marcey, David. Submitted by: Marcey, David. (Entry 105). Submitted on Jun 17, 2001.
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hirudin :
Structural Biochemistry of Blood Coagulation. (Walters, D. Eric)
Histrionicotoxin :
Molecule of the Month/University of Bristol. (May, Paul (editor))
HIV :
The Rational Basis of Drug Design. (Walters, D. Eric)
HIV :
BioMolecular Explorer 3D: Resources for High School Biology. (Reichsman, Frieda; Eric Martz)
HIV gp120 :
Viral Antigens (at The Online Macromolecular Museum). (Mazur, Eric; Marcey, David)
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HIV protease :
Macromolecular Visualization Laboratory Exercise. (Kahn, Kalju)
HIV protease :
The Lycoming College Macromolecular Modeling and Bioinformatics Page. (Newman, Jeff)
HIV Reverse Transcriptase :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
HIV Reverse Transcriptase :
Biomolecules at Kenyon College. (Students, Kenyon College; Site Director, Joan Slonczewski) (English; CopG auf Deutch)
HIV-1 :
HIV-1 Integrase (at The Online Macromolecular Museum). (Walsh, Matthew; Marcey, David)
HIV-1 dimer :
Biomolecules at Kenyon College. (Students, Kenyon College; Site Director, Joan Slonczewski) (English; CopG auf Deutch)
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HIV-1 Integrase :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
HIV-1 Integrase (at The Online Macromolecular Museum):
Cross-indexing terms: DNA recombination; integrase; HIV-1; DNA binding.
The integration of HIV-1 DNA into the host chromosome is achieved by the integrase protein performing a series of DNA cutting and joining reactions. This Chime-based exhibit focuses on the catalytic core domain and minimal DNA binding domain of HIV-1 integrase.
Authors: Walsh, Matthew; Marcey, David. Submitted by: Marcey, David. (Entry 104). Submitted on Jun 17, 2001.
HIV-1 Nef Protein (at The Online Macromolecular Museum):
Cross-indexing terms: Nef; CD4 downregulation; SH3 domain interaction; retroviral Nef.
Nef is a viral protein that interacts with host cell signal transduction proteins to provide for long term survival of infected T cells and for destruction of non-infected T cells by inducing apoptosis. Nef also advances the endocytosis and degradation of cell surface proteins, including CD4 and MHC proteins. This Chime-based exhibit focuses on the structural features of the Nef core domain that provide for its mutiple functions.
Authors: Somple, Maggie; Silva, Nathan; Marcey, David. Submitted by: Marcey, David. (Entry 119). Submitted on Jun 20, 2001. Last revised on Jun 20, 2001.
HIV-1 Protease :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
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HIV-1 Protease (at The Online Macromolecular Museum):
Cross-indexing terms: viral protease; retroviral protease; protease, HIV-1.
HIV-1 Protease (PR) hydrolyzes viral polyproteins into functional protein products that are essential for viral assembly and subsequent activity. This maturation process occurs as the virion buds from the host cell. This Chime-based exhibit focuses on the structure-function relationships of PR.
Authors: Mana, Miyeko; Marcey, David. Submitted by: Marcey, David. (Entry 118). Submitted on Jun 18, 2001.
HIV-1 Reverse Transcriptase (at The Online Macromolecular Museum):
Cross-indexing terms: reverse transcriptase and non-nucleoside inhibitors thereof; retrovirus; azt.
The enzyme reverse transcriptase (RT) is used by retroviruses to transcribe their single-stranded RNA genome into single-stranded DNA and to subsequently construct a complementary strand of DNA, providing a DNA double helix capable of integration into host cell chromosomes. This exhibit focuses on the structure-function relationships of the HIV-1 RT. The action of some RT inhibitors is examined.
Authors: Goldman, Matthew; Marcey, David. Submitted by: Marcey, David. (Entry 108). Submitted on Jun 17, 2001.
HIV-protease inhibitor :
The Rational Basis of Drug Design. (Walters, D. Eric)
HIV-protease inhibitor :
BioMolecular Explorer 3D: Resources for High School Biology. (Reichsman, Frieda; Eric Martz)
HLA (human MHC) :
Major Histocompatibility Complex. (Martz, Eric)
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HMG-CoA :
Isoprenoid Biosynthesis Pathway. (Warren, L. Van)
Holliday Junction :
RecA Protein (at The Online Macromolecular Museum). (Heerssen, Heather; Downs, Aaron; Marcey, David)
homeodomain :
Biomodel. (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish)
homeodomain proteins :
Nucleic Acid Structure Tutorials. (Nolan, Jim)
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homology modelling :
AHo's Amazing Atlas of Antibody Structure. (Honegger, Annemarie)
hook, flagellar :
Flagellar Hook, Bacterial -- A Molecular Universal Joint. (Martz, Eric)
horseradish peroxidase :
Protein Structure Analysis Using Internet Tools: A Tutorial Using Peroxidase. (Rojas, Nina Rosario L.; Quiambao, Paul Rosby M.)
How to Create New Chime Tutorials:
Cross-indexing terms: scripting methods in Chime; Chime methods and tools; authoring new Chime websites, methods; methods for constructing new Chime websites and scripts.
At : Methods and tools for constructing new tutorials and websites with Chime are gathered in this section of the World Index of Molecular Visualization Resources. This separates them from the present section, which is for "Ready to Use" tutorials.
Author: Martz, Eric Submitted by: the author. (Entry 124). Submitted on Jul 14, 2001. Last revised on Oct 3, 2004.
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Human hnRNP A1 :
Structures for Molecular Biology. (McClure, William)
hydrogen bonding :
Magnesium Adenosine Triphosphate (MgATP) Binding to an Enzyme. (Bruist, Michael)
hydrogen bonding, Watson-Crick :
DNA Structure. (Martz, Eric) (English, German, Portuguese, Spanish)
hydrogen bonding, Watson-Crick :
DNA Structure (with Jmol). (Herraez, Angel; Martz, Eric)
hydrogen bonds :
Protein Secondary Structure, versions 1.0, 2.0, 3.0. (Reichsman, Frieda; Driscoll, Tim)
hydrogen bonds :
Chemical Bonds and Protein Structure (at The Online Macromolecular Museum). (Marcey, David)
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hydrogen bonds, finding :
NonCovalent Bond Finder (NCBF). (Martz, Eric)
hydrogen peroxide :
Catalase (at The Online Macromolecular Museum). (Boon, Elizabeth; Downs, Aaron; Marcey, David)
hydrophobic bonds :
Chemical Bonds and Protein Structure (at The Online Macromolecular Museum). (Marcey, David)
hydrophobic interactions :
Magnesium Adenosine Triphosphate (MgATP) Binding to an Enzyme. (Bruist, Michael)
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hydrophobic interactions, finding :
NonCovalent Bond Finder (NCBF). (Martz, Eric)
hydroxylamine oxidoreductase :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
hyperforin :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
hyperthermophilic archaeon :
Rubisco: a first look at the mechanism. An experiment in molecular visualisation. (Nixon, John)
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hypervariable regions, immunoglobulin :
Antibody Recognition of Antigen (at The Online Macromolecular Museum). (Marcey, David)
hypervariable residues :
ConSurf Server for the Identification of Functional Regions in Proteins by Surface Mapping of Phylogenetic Information. (Glaser, Fabian; Ben-Tal, Nir; Pupko, Tal; Martz, Eric)
I-helix :
Cytochrome P450 3D structures page. (Nelson, David)
icosahedral capsid structure :
SV40 capsid structure and assembly. (Welte, Stefan)
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IgG :
Antibody. (Martz, Eric)
IgG immunoglobulin :
Molecular Science Lab. (Oberholser, Karl)
Images of Glycolysis Intermediates:
Cross-indexing terms: glycolysis.
In a frames format, the reactions of glycolysis are shown as Chime displays of the substrates, products and cofactors. Links to the fermentation fates of pyruvate and to similar displays of TCA cycle intermediates are provided.
Author: McClure, William Submitted by: the author. (Entry 26). Submitted on Jun 1, 2000.
Images of TCA Cycle Intermediates:
Cross-indexing terms: Tricarboxylic acid cycle; Citric acid cycle; Kreb's cycle.
In a frames format, the reactions of the TCA Cycle are shown as Chime displays of the substrates, products and cofactors.
Author: McClure, William Submitted by: the author. (Entry 30). Submitted on Jun 1, 2000.
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immune system, MHC :
Major Histocompatibility Complex. (Reichsman, Frieda)
immunoglobulin :
Biomodel. (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish)
immunoglobulin :
AHo's Amazing Atlas of Antibody Structure. (Honegger, Annemarie)
immunoglobulin and Ig domains :
Antibody. (Martz, Eric)
immunoglobulin fold :
Immunoglobulin Structure (at The Online Macromolecular Museum). (Marcey, David)
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Immunoglobulin G (Igg.pdb), an all-β antibody protein :
Protein Structures List. (McClure, William)
Immunoglobulin Structure :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
Immunoglobulin Structure (at The Online Macromolecular Museum):
Cross-indexing terms: antibody structure; immunoglobulin fold.
This Chime-based exhibit provides an introduction to immunoglobulin structure, including tetramer structure, the structure of the immunoglobulin fold, and the structure of the variable region.
Author: Marcey, David Submitted by: the author. (Entry 116). Submitted on Jun 18, 2001.
immunoglogulin binding :
Antibody Recognition of Antigen (at The Online Macromolecular Museum). (Marcey, David)
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indinavir :
The Rational Basis of Drug Design. (Walters, D. Eric)
influenza hemagglutinin :
Viral Antigens (at The Online Macromolecular Museum). (Mazur, Eric; Marcey, David)
influenza hemagglutinin, morph :
Morpher, Protein. (Martz, Eric)
Infrared spectra, animations of vibrational modes:
Cross-indexing terms: animations of vibrations, infrared spectra; XYZ files used for infrared vibrations; vibrational modes, infrared spectra, animated.
The IR spectrum of acetophenone is given as an example (rendered by Chime from a data file in the JCAMP format). Clicking on a peak animates the corresponding vibrational mode in a Chime-rendering of the molecule. Links to additional resources detail the methods employed to construct such displays, as well as resources that highlight bonds or atoms corresponding to peaks in MS or NMR spectra, and IR spectra for a series of additional molecules. Downloadable for off-line use, local installation or modification.
Authors: Motyka, Eric; Lahti, Paul; Lancashire, Robert J.. Submitted by: Martz, Eric. (Entry 56). Submitted on Aug 8, 2000. Last revised on Jul 1, 2002.
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inhibitor, protease :
The Rational Basis of Drug Design. (Walters, D. Eric)
Innovative framing approach to CHIME based tutorials :
Rubisco: a first look at the mechanism. An experiment in molecular visualisation. (Nixon, John)
Insulin receptor :
The Lycoming College Macromolecular Modeling and Bioinformatics Page. (Newman, Jeff)
integrase :
HIV-1 Integrase (at The Online Macromolecular Museum). (Walsh, Matthew; Marcey, David)
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integration host factor :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
integrin :
Fibronectin (at The Online Macromolecular Museum). (Ward, Michael; Marcey, David)
integrin CD11b MIDAS domain, morph :
Morpher, Protein. (Martz, Eric)
Interactive Quercetin 2,3-Dioxygenase Presentation:
Cross-indexing terms: dioxygenase; copper; glycosylation; cupin; quercetin.
Chime-based presentation of the (crystal) structure of the copper-containing quercetin 2,3-dioxygenase from Aspergillus japonicus. Description of monomer and dimer structure with extensive glycosylation, the active site with substrate and homology with other enzymes.
Script buttons invoke "movies"; in addition general commands can also be executed by clicking a button. Resources (literature, PDB links) included.
Author: Pijning, T Submitted by: the author. (Entry 140). Submitted on Sep 10, 2002. Last revised on Sep 11, 2002.
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Introduction to Protein Structure:
Cross-indexing terms: protein structure; peptide structure; amino acid chemistry; primary structure; secondary structure; tertiary structure; quarternary structure; alpha helix; beta sheet.
This CHIME-enhanced site is meant for beginning biochemistry students. It covers every thing from the acid-base chemistry of the amino acids through the hierarchy of protein structure (i.e. primary to quarternary) much as the typical undergraduate biochemistry textbook does except that "live", interactive CHIME structures are used throughout.
Author: Gorga, Frank Submitted by: the author. (Entry 87). Submitted on Mar 8, 2001.
Introduction to Protein Structure, Part I:
Cross-indexing terms: structure, protein, primary, secondary; polypeptide; sidechain; peptide bond; alpha-helix; ribbon; beta pleats; primary structure; secondary structure; tertiary structure; quaternary structure; hemoglobin; myoglobin.
A custom Web-based application which uses a discovery-based approach to examining protein structure. In part I, primary and secondary structures are introduced by analyzing simple polypeptides. This forms the springboard for the analysis of more complex proteins. Visualization employs Chime.
Author: Bragin, Victoria (Vicki) Submitted by: the author. (Entry 62). Submitted on Aug 17, 2000. Last revised on Mar 19, 2001.
intron :
XdomView: A Chime-based Graphical Tool for Protein Domain and Exon Position Visualization. (Gopalan, Vivek; Shoba Ranganathan; Tan Tin Wee)
intron :
XdomView: A Chime-based Graphical Tool for Protein Domain and Exon Position Visualization. (Gopalan, Vivek; Shoba Ranganathan; Tan Tin Wee)
intron evolution :
XdomView: A Chime-based Graphical Tool for Protein Domain and Exon Position Visualization. (Gopalan, Vivek; Shoba Ranganathan; Tan Tin Wee)
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introns :
Sickle Cell Anemia: Understanding the Molecular Biology. (Sabo, John; Lynch, Jamie; Raineri, Deanna)
ion channel :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
ionic bonds :
Chemical Bonds and Protein Structure (at The Online Macromolecular Museum). (Marcey, David)
Ionophores: Gramicidin & Valinomycin :
Membrane Channel & Pump Structures. (McClure, William)
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IPA :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
iron-sulfur proteins :
Redox Proteins. (Hansson, Orjan)
isomerism, constitutional :
Web-Based Chemical Investigations. (Bragin, Victoria (Vicki))
Isopentenyl pyrophosphate :
Isoprenoid Biosynthesis Pathway. (Warren, L. Van)
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Isoprenoid Biosynthesis Pathway:
Cross-indexing terms: Acetyl-CoA; HMG-CoA; Mevalonate; pyrophosphate; Isopentenyl pyrophosphate; Geranyl pyrophosphate; Farnesyl pyrophosphate; Squalene; Lanosterol; Desmosterol; Cholesterol; Steroids.
Chime is used to illustrate each step in this pathway, including the conversion of acetyl-CoA to cholesterol and the abundance of intermediate forms that are vectored off for other purposes, including isoprenylated proteins such as rhodopsin kinase.
Author: Warren, L. Van Submitted by: the author. (Entry 59). Submitted on Aug 15, 2000.
jasmonic acid :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
java :
Structural Alignment Program for Proteins. (Gille, Christoph)
jmol :
Structural Alignment Program for Proteins. (Gille, Christoph)
jmol :
DNA Structure (with Jmol). (Herraez, Angel; Martz, Eric)
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Johanniskraut :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
Jun :
Molecules and Structures Homepage. (Gasser, Charles)
K+-Channel (1bl8.pdb), an ion-selective pore :
Protein Structures List. (McClure, William)
K-12 education :
Molecular Visualization Resources for Project VISM. (Klevickis, Cindy)
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K-helix :
Cytochrome P450 3D structures page. (Nelson, David)
KcsA K+ Channel (1k4c.pdb) :
Membrane Channel & Pump Structures. (McClure, William)
kinase, protein :
Protein Kinase CKII. (Glover III, Claiborne)
kinase, tyrosine :
Explore the c-Src tyrosine kinase. (Engen, John R; Superti-Furga, Giulio)
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KirBac1.1 K+ Channel (1p7b.pdb) :
Membrane Channel & Pump Structures. (McClure, William)
Kreb's cycle :
Images of TCA Cycle Intermediates. (McClure, William)
KvAP, a Voltage-Gated K+ Channel (1orq.pdb, 1ors.pdb) :
Membrane Channel & Pump Structures. (McClure, William)
lab exercise :
Small Molecule Lab Exercise. (White, Brian)
lab exercise :
DNA quizzer. (White, Brian)
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lac repressor :
Biomolecules at Kenyon College. (Students, Kenyon College; Site Director, Joan Slonczewski) (English; CopG auf Deutch)
lac repressor :
Lac Repressor: Biochemistry in 3D. (Driscoll, Timothy)
lac repressor :
BioMolecular Explorer 3D: Resources for High School Biology. (Reichsman, Frieda; Eric Martz)
Lac repressor bending DNA operon:
Cross-indexing terms: bending of DNA; animations; Chime; lesson plan.
At : Animations of the lac repressor bending its DNA operon when nonspecific binding to DNA converts to specific binding. Several animations that can be viewed in MDL Chime highlight different aspects of the specific binding process. One shows 5 hydrogen bonds forming in the major and minor grooves representing sequence-specific recognition. The animations were saved from Protein Explorer using a linear-interpolation morph, which is provided for direct exploration in Protein Explorer. Questions are provided for students.
Author: Martz, Eric Submitted by: the author. (Entry 156). Submitted on Oct 3, 2004. Last revised on Oct 3, 2004.
Lac Repressor: Biochemistry in 3D:
Cross-indexing terms: transcription; lac repressor; lacR; transcriptional regulation; gene regulation in bacteria.
An in-depth investigation into the function of this classic bacterial gene regulator. Includes animations showing the binding of lacR to DNA operators, core dimer and tetramer interactions, and structural effects of inducer binding. follow the allosteric effects of inducer binding as they propagate through the core to the headpiece, and affect the interaction between lacR and its operator sites. One of several detailed Chime structure-function tutorials that accompany Lehninger Principles of Biochemistry. All of these tutorials require Chime and Netscape Communicator 4.5-4.79, and use actual structure files from various sources. all tutorials are extensively annotated with text and citations, and offer powerful, user-friendly controls to supplement the Chime animations.
Author: Driscoll, Timothy Submitted by: the author. (Entry 141). Submitted on Sep 18, 2002.
lacR :
Lac Repressor: Biochemistry in 3D. (Driscoll, Timothy)
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lactase :
BioMolecular Explorer 3D: Resources for High School Biology. (Reichsman, Frieda; Eric Martz)
lactate :
The Glycolytic Cycle. (Warren, L. Van)
lactate dehydrogenase :
The Glycolytic Cycle. (Warren, L. Van)
Lactate Dehydrogenase (1ldm.pdb), a two-domain protein with a nucleotide-binding motif :
Protein Structures List. (McClure, William)
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lactate fermentation :
Student Webpapers: The Structure-Function Relationships for the Enzymes in the Glycolytic and Lactate Fermentation Pathways. (Chem406 Class, Fall 1999, U Wisc-Eau Claire)
LamB Porin :
Porin Proteins (at The Online Macromolecular Museum). (Flammer, Kristin; Downs, Aaron; Marcey, David)
lambda receptor :
Porin Proteins (at The Online Macromolecular Museum). (Flammer, Kristin; Downs, Aaron; Marcey, David)
lambda repressor :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
lambda repressor :
Molecules and Structures Homepage. (Gasser, Charles)
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Lanosterol :
Isoprenoid Biosynthesis Pathway. (Warren, L. Van)
Large Ribosomal Subunit Tour:
Cross-indexing terms: ribosome, large subunit; translation; ribozyme; rRNA; peptide bond synthesis; RNA, ribosomal; 50S ribosomal subunit.
A Chime-based tour of the large ribosomal subunit suitable for college-level classes. Highlights the key features of the large subunit such as the site of peptide bond synthesis and the polypeptide exit tunnel. Demonstrates how the ribosome seems to be a ribozyme and shows one theory on how the chemistry works. Based on the structure of the Archaeal large ribosomal subunit reported in 2000 by Steitz, Moore, and coworkers.
Author: Decatur, Wayne Submitted by: the author. (Entry 121). Submitted on Jun 21, 2001. Last revised on Nov 7, 2003.
Large Ribosomal Subunit Tour for Specialists:
Cross-indexing terms: ribosome, large subunit for specialists; RNA, ribosomal; rRNA; translation; ribozyme.
An extensive, Chime-based tour of the Archaeal Large Ribosomal Subunit for specialists. The full tour requires Netscape Communicator (Navigator) 4.5-4.7 but there is a sample tour that covers the key features that works with Chime in other browsers on computers running Microsoft Windows. The full tour interface has been designed with the issues that the large coordinate data files entail in mind. Be aware that you need a good connection to the internet for this to work and not be frustrating. Several of the structure files used in the tour are in excess of 1 Mb.
Author: Decatur, Wayne Submitted by: the author. (Entry 82). Submitted on Dec 4, 2000. Last revised on Jun 21, 2001.
Lehninger's Principles of Biochemistry :
Protein Architecture at Biochemistry in 3D. (Driscoll, Timothy; Reichsman, Frieda)
Lehninger's Principles of Biochemistry :
G Proteins (Trimeric): Molecular On/Off Switches, at Biochemistry in 3D. (Reichsman, Frieda; Driscoll, Timothy)
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lesson plan :
Amino Acid Identification Quiz. (McClure, William)
lesson plan :
Nucleotide Identification Quiz. (McClure, William)
lesson plan :
Molecular Models for Biochemistry at CMU. (McClure, William)
lesson plan :
Student Webpapers: The Structure-Function Relationships for the Enzymes in the Glycolytic and Lactate Fermentation Pathways. (Chem406 Class, Fall 1999, U Wisc-Eau Claire)
lesson plan :
The 20 common amino acids. (Bragin, Victoria (Vicki); Johnston, Wendie)
lesson plan :
DNA quizzer. (White, Brian)
lesson plan :
Biomolecular Structures. (Hansson, Orjan)
lesson plan :
Redox Proteins. (Hansson, Orjan)
lesson plan :
DNA Polymerase I from Thermus aquaticus. (Bruist, Michael)
lesson plan :
Amino Acid Structure Quiz. (McClure, William)
lesson plan :
Macromolecular Visualization Laboratory Exercise. (Kahn, Kalju)
lesson plan :
Water Simulation. (Martz, Eric)
lesson plan :
Lac repressor bending DNA operon. (Martz, Eric)
lesson plan :
BioMolecular Explorer 3D: Resources for High School Biology. (Reichsman, Frieda; Eric Martz)
lesson plan, amino acid quizzer :
Amino Acid Quizzer. (Martz, Eric; White, Brian)
lesson plan, antibody :
Antibody. (Martz, Eric)
lesson plan, MHC :
Major Histocompatibility Complex. (Martz, Eric)
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lesson plans :
Molecular Visualization Resources for Project VISM. (Klevickis, Cindy)
lesson plans :
Web-Based Chemical Investigations. (Bragin, Victoria (Vicki))
lesson plans :
Molecular Science Lab. (Oberholser, Karl)
lesson plans :
The Zinc Finger: A Protein Domain that Binds Specific DNA Sequences. (Bruist, Michael)
leucine zipper :
Biomodel. (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish)
leucine zippers :
Chime Square. (Niederhoffer, Eric)
leucine zippers :
Protein/DNA interactions. (Gibson, Andrew; Sims, P. F. G.)
LexA protease :
RecA Protein (at The Online Macromolecular Museum). (Heerssen, Heather; Downs, Aaron; Marcey, David)
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ligand activation :
The E. coli trp Repressor Chime Movie. (Lawson, Cathy)
ligand binding :
Molecular Science Lab. (Oberholser, Karl)
ligand-protein complexes :
Noncovalent Interactions in Proteins. (Cox, Ricky)
light harvesting complex :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
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links to Chime sites :
Chime: Great Sites. (MDL Information Systems, Inc.)
links to other sites with graphics displays related to biochemistry :
Molecular Models for Biochemistry at CMU. (McClure, William)
lipid bilayer :
Biomodel. (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish)
lipid bilayers :
BioMolecular Explorer 3D: Resources for High School Biology. (Reichsman, Frieda; Eric Martz)
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Lipid Bilayers and the Gramicidin Channel:
Cross-indexing terms: gramicidin channel in lipid bilayer; cholesterol; phosphatidyl choline; bilayer, lipid; phospholipid bilayers.
At : This Chime presentation shows cholesterol, phosphatidyl choline, and then illustrates the assembly of hydrated crystalline bilayer model. Results of two molecular dynamics simulations (by Helmut Heller et al.) are shown, resulting in gel- and fluid-like conformations. Then the gramicidin channel is shown in a hydrated bilayer of phosphatidyl ethanolamine (modeled by Serge Crouzy et al.). Adapted to Chime in 2001 by Angel Herraez from the 1997 RasMol "Movie" Script by Eric Martz. Also available in Spanish. Links are provided for further exploration of these models in Protein Explorer.
Authors: Martz, Eric; Herraez, Angel. Submitted by: the author. (Entry 90). Submitted on Apr 1, 2001. Last revised on Oct 3, 2004.
LSD :
Molecule of the Month/University of Bristol. (May, Paul (editor))
luciferase :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
lysozyme :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
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Lysozyme & substrate :
Molecules for Modern/Cell Biology. (McClure, William)
Macromolecular Visualization Laboratory Exercise:
Cross-indexing terms: DNA; transfer RNA; HIV protease; tRNA synthetase; rhinovirus; lesson plan; SYBYL; RasMol; SGI workstations.
The tutorial with accompanyng exercises illustrates the kind of questions students can answer with the help of computer modeling. It focuses on analysis of molecular structures and shows how to create images that help to illustrate important features of macromolecules. The tutorial also teaches that biological macromolecules come in very different shapes and sizes.
The tutorial also teaches a few technical skills that are commonly used while working with computer visualization programs. First, it shows some typical capabilities of the visualization programs SYBYL and RasMol. It also teaches about image capture and manipulation programs on SGI workstations, and shows how one can send images created on an UNIX computer to other people.
The tutorial assumes access to modeling programs SYBYL and RasMol. The tutorial is part of a formal coursework for biochemistry majors at UCSB.
Author: Kahn, Kalju Submitted by: the author. (Entry 150). Submitted on May 16, 2004.
MAD :
Molecules and Structures Homepage. (Gasser, Charles)
MADS box :
Molecules and Structures Homepage. (Gasser, Charles)
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mage :
Rubisco: a first look at the mechanism. An experiment in molecular visualisation. (Nixon, John)
Magnesium Adenosine Triphosphate (MgATP) Binding to an Enzyme:
Cross-indexing terms: dethiobiotin synthetase; Mg-ATP binding; substrate binding; hydrogen bonding; hydrophobic interactions; salt-briges.
This page illustrates how an enzyme binds specifically to a substrate using dethiobiotin synthetase from E. coli. The initial space-filling view shows ATP buried on the surface of an enzyme. An animation then zooms into the active site as all protein residues not binding ATP are removed. The hydrophobic interactions, hydrgen bonding, and ionic interactions can be color coded. Monitors (lines) indicating hydrogen bonds and salt bridges can be toggled on and off. A simple rigid body animation shows how ATP might move into this site from solution.
Author: Bruist, Michael Submitted by: the author. (Entry 139). Submitted on Sep 10, 2002.
major groove :
DNA Structure (at The Online Macromolecular Museum). (Marcey, David)
major histocompatibility class I :
Garrett & Grisham Interactive Biochemistry. (Garrett, R. H.; Grisham, C. M.)
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Major Histocompatibility Complex:
Cross-indexing terms: MHC classes I and II; virus peptides, binding to MHC; epitopes, T-cell; H-2 (mouse MHC); HLA (human MHC); lesson plan, MHC.
At : A tutorial on MHC structure in Chime including an introduction to stick, ball and stick, spacefill renderings, peptides and backbones, disulfide bond renderings, MHC class I secondary and tertiary structure, beta-2 microglobulin, CD8-binding site, papain cleavage site, the peptide-binding cleft, Sendai nucleoprotein nonamer and vesicular stomatitus virus nucleoprotein octamer binding to H-2Kb with comparison of their T-cell epitopes. MHC class II secondary and tertiary structure and peptide binding (HLA-DR1 with influenza hemagglutinin 13-mer). Buttons can be pushed in any order yet always give the same images. Font size can be dymanically changed for large audiences. The utilities menu enables recentering, atom identification, measuring distances, and changing background color from black to white for printing. A list of questions is provided which can be printed and handed out to a class as a focus worksheet (lesson plan). Downloadable for off-line use, local installation or modification.
Author: Martz, Eric Submitted by: the author. (Entry 15). Submitted on May 28, 2000. Last revised on Oct 3, 2004.
Major Histocompatibility Complex:
Cross-indexing terms: MHC proteins; immune system, MHC.
This Chime tutorial is a comparative exploration of Class I and II MHC proteins and their bound peptdes. Major similarities and differences are elucidated in side-by-side comparisons (using two Chime windows next to each other). Each class of MHC is also explored in depth individually. Close attention to binding pockets and specificity of binding. Use of surface representations to illustrate binding clefts and anchor pockets. Smooth transitions between views show their relationships clearly. The interface is easy to use for students and novices, but advanced users can modify the images with menus, or enter Chime commands.
Author: Reichsman, Frieda Submitted by: the author. (Entry 92). Submitted on Jun 5, 2001.
malaria :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
Maltoporin :
Porin Proteins (at The Online Macromolecular Museum). (Flammer, Kristin; Downs, Aaron; Marcey, David)
Maltoporin (2mpr.pdb), a trimeric sugar transporter in bacteria :
Protein Structures List. (McClure, William)
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MCM-41 :
Molecule of the Month/University of Bristol. (May, Paul (editor))
Melatonin :
Molecule of the Month/University of Bristol. (May, Paul (editor))
Membrane Channel & Pump Structures:
Cross-indexing terms: KcsA K+ Channel (1k4c.pdb); MthK K+ Channel (1lnq.pdb); KvAP, a Voltage-Gated K+ Channel (1orq.pdb, 1ors.pdb); KirBac1.1 K+ Channel (1p7b.pdb); EcClC Chloride Channel (1ots.pdb, 1otu.pdb); E. coli Glycerol Channel (1fx8.pdb, 1ldi.pdb); AQP1 Aquaporin Channel (1j4n.pdb); MscS, Mechanosensitve Small Conductance Channel (1mxm.pdb); MscL, Mechanosensitve Large Conductance Channel (1msl.pdb); Ionophores: Gramicidin & Valinomycin; SERCA1 Ca2+ Pump (1eul.pdb, 1iwo.pdb); Bacteriorhodopsin (1c3w.pdb, 1dze.pdb).
An index table of structures for biochemistry courses. PubMed entries and Chime displays of the structures can be viewed by following the links provided. (PDB ID) for the structures displayed are shown above.
Author: McClure, William Submitted by: the author. (Entry 146). Submitted on Jun 27, 2003.
Membranes :
Molecules for Modern/Cell Biology. (McClure, William)
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Mescaline :
Molecule of the Month/University of Bristol. (May, Paul (editor))
Met J repressor :
Protein/DNA interactions. (Gibson, Andrew; Sims, P. F. G.)
Met-enkephalin :
Side-by-Side Amino Acid Viewer. (McClure, William)
metabolism :
Chime Square. (Niederhoffer, Eric)
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Metal ion-induced catalysis :
DNA Polymerase of Bacteriophage T7 (at The Online Macromolecular Museum). (Ward, Michael; Marcey, David)
metalloproteins :
Chime Square. (Niederhoffer, Eric)
methods for constructing new Chime websites and scripts :
How to Create New Chime Tutorials. (Martz, Eric)
Methylase, DNA :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
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methyltransferases :
HhaI DNA Methyltransferase (at The Online Macromolecular Museum). (Douglass, Ben; Downs, Aaron; Marcey, David)
Mevalonate :
Isoprenoid Biosynthesis Pathway. (Warren, L. Van)
Mg-ATP binding :
Magnesium Adenosine Triphosphate (MgATP) Binding to an Enzyme. (Bruist, Michael)
MHC class I :
Garrett and Grisham Interactive Biochemistry Structure Tutorials. (Caras, James)
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MHC classes I and II :
Major Histocompatibility Complex. (Martz, Eric)
MHC proteins :
Major Histocompatibility Complex. (Reichsman, Frieda)
micromolecules :
Molecular Visualization Resources for Project VISM. (Klevickis, Cindy)
minor groove :
DNA Structure (at The Online Macromolecular Museum). (Marcey, David)
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mismatch repair :
MutS DNA Repair Protein (at The Online Macromolecular Museum). (Stoffregen, Eric; Marcey, David)
mismatch repair :
MutH (at The Online Macromolecular Museum). (Carney, Jessica; Silva, Nathan; Marcey, David)
mitochondrial respiratory chain complexes :
Molecular Science Lab. (Oberholser, Karl)
MMDB :
XdomView: A Chime-based Graphical Tool for Protein Domain and Exon Position Visualization. (Gopalan, Vivek; Shoba Ranganathan; Tan Tin Wee)
Molecular Models for Biochemistry at CMU:
Cross-indexing terms: lesson plan; tutorials on molecular structures; quizzes using Chime displays and GIF images; links to other sites with graphics displays related to biochemistry.
Index page with links to tutorials and quizzes that are based on Chime and RasMol images of the molecules and macromolecules found in biochemistry. They are intended to complement standard biochemistry texts where more explanation is provided, but where interactive 3-D images of the molecules are not available. Links to various pages used in courses at Carnegie Mellon University.
Author: McClure, William Submitted by: the author. (Entry 32). Submitted on Jun 1, 2000.
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Molecular Science Lab:
Cross-indexing terms: myohemerythrin; Bence-Jones protein REI monomer & dimer; BPTI; trypsinogen-BPTI; acetylcholinesterase inhibitors; myoglobin; hemoglobin; acetylcholinesterase mechanism; cytochrome bc1; cytochrome c oxidase; mitochondrial respiratory chain complexes; serine esterase; IgG immunoglobulin; trypsin inhibitor; acetylcholinesterase-decamethonium; acetylcholinesterase-tacrine; acetycholinesterase-edrophonium; acetylcholinesterase- m-(N,N,N-trimethylammonio)trifluoroacetophenone; globular proteins; fibrous proteins; ligand binding; lesson plans.
Contains exercises that uses Protein Explorer to study the structure and function of proteins. Some exercises contain buttons that control the Chime display, while others are without buttons but have suggestions in ways to use PE to investigate the structure of the protein. Illustrations and tips are given on the use of PE. Major topics covered are introduction to fibrous and globular proteins, ligand protein binding, myoglobins, hemoglobins, enzymatic mechanisms which includes several mitochondrial respiratory complexes.
Author: Oberholser, Karl Submitted by: the author. (Entry 123). Submitted on Jul 12, 2001.
molecular surface :
Accessible, molecular and Van der Waals surfaces explained. (Krieger, Elmar)
Molecular Visualization Resources for Project VISM:
Cross-indexing terms: Bowen's Reaction Series; small molecules; micromolecules; lesson plans; K-12 education.
VISM is an NSF-funded program to promote the use of computer visualization resources in teaching science and math, especially for 6-12 students. This page is the VISM resource page for using RasMol and Chemscape Chime to teach Geology, Earth Science, Environmental Sciences and other Physical Sciences, as well as Biology and Chemistry. The page is under continual construction. Currently, there is one model lesson plan for "the Bowen's Reaction Series." Other lesson plans are under development. We are interested in developing a repository of pdb files for molecules related to physical sciences. However, there will also be lesson plans for Biology and Chemistry.
Author: Klevickis, Cindy Submitted by: the author. (Entry 49). Submitted on Jul 20, 2000.
Molecular Visualizations on Apoptosis: (Spanish )
Cross-indexing terms: apoptosis, programmed cell death, caspases, NF-kappa B, Ik-B, bcl-2, IAP.
Molecular Tutorials based on chime on macromolecules involved in apoptosis, in Spanish. Tutorials available are on the structure of caspases, the proteases responsible for the execution of apoptotic program. It shows the quaternary structure, the structure of active center and its interaction with pseudosubstrates. Also available is a tutorial on NF-Kappa B, a transcription factor system which has been involved in the survival pathways from apoptosis. Nf-kappa B when activated by translocation to the nucleus transactivate survival genes as bcl-2 family members or IAP genes (specific inhibitors of caspases). The structure of the transcription factor bound to the DNA responsive element is shown whith details of the contacts between both molecules. Also shown is the interaction between NF-Kappa B and IK-B, the physiological inhibitor of NF-Kappa B.
Authors: Pons, Gabriel; Gil, Joan. Submitted by: the author. (Entry 91). Submitted on May 4, 2001.
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Molecule of the Month/Oxford University:
Short overviews of the history and chemistry of diverse molecules, written by various authors. In each month, a different molecule is featured at each of the MOTM sites. Chime is often employed.
Author: Harrison, Karl (editor) Submitted by: Martz, Eric. (Entry 6). Submitted on May 24, 2000.
Molecule of the Month/University of Bristol:
Cross-indexing terms: Cisplatin; Thalidomide; Histrionicotoxin; Chlorophyll; Melatonin; cis-g-Irone; Frankincense; Boswellic Acid; DNA; Tamoxifen; Tetrodotoxin; Psilocybin; Mescaline; Anatoxin; Salbutamol; Zyban; Bupropion; Nitrous oxide; Adrenaline; Staurosporine; Ptaquiloside; Sarin, cubane; LSD; Polythiophene; Ferritin; Saxitoxin; Water; Formaldehyde; Finasteride; Mustard Gas; Proline; MCM-41; Ozone; Sulfanilamide; Adenosine Triphosphate; ATP; ChemSymphony.
Short overviews of the history and chemistry of diverse molecules, written by various authors. In each month, a different molecule is featured at each of the MOTM sites. Chime is often employed.
Author: May, Paul (editor) Submitted by: Miller, Mitch. (Entry 5). Submitted on May 24, 2000. Last revised on Jul 21, 2000.
Molecules and Structures Homepage:
Cross-indexing terms: amino acid; disulfide bond; nucleosome; TATA-binding protein; transcription factor; Glucocorticoid receptor; GCN4; Engrailed; Gal4; Lambda Repressor; TFIIIA; MAD; MyoD; Zif; NFAT; Fos; Jun; NFKappaB; Serum Response Factor (SRF); MADS box; SP1.
Lead-in page to structures of amino acids in Chime format, Chymotrypsin tutorial in chime format, and set of pages showing a varitey of regulatory transcription factors and TATA-binding protein in Chime format with buttons for different views. Compare structures of B- and X-DNA.
Author: Gasser, Charles Submitted by: the author. (Entry 127). Submitted on Sep 21, 2001. Last revised on Sep 21, 2001.
Molecules for Modern/Cell Biology:
Cross-indexing terms: Elements; H2O cluster; Functional Groups; Enantiomers of glyceraldehyde; Fats: Glycerol & Fatty Acids; Phospholipid; Membranes; Bacteriorhodopsin: A membrane-spanning protein; Cholesterol; Sucrose -> Fructose & Glucose; Amino Acids & Peptides; α-Helix & β-Sheet in a Small Protein; Lysozyme & substrate; Hemoglobin; Nucleotides: A, C, G, T, & U; DNA & RNA; ATP; NAD+; CAP (cAMP binding protein) & DNA; cAMP.
An index table of figures in common textbooks for introductory biology or cell biology courses where molecular structures are pictured. Chime displays of the structures can be viewed by following the links provided.
Author: McClure, William Submitted by: the author. (Entry 19). Submitted on Jun 1, 2000.
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Molecules of the Month/Imperial College:
Short overviews of the history and chemistry of diverse molecules, written by various authors. In each month, a different molecule is featured at each of the MOTM sites.
Author: Rzepa, Henry (editor) Submitted by: Martz, First. (Entry 4). Submitted on May 24, 2000.
Molecules, finding :
PDB Lite. (Martz, Eric; Prilusky, Jaime)
molecules, sources of, organic (PDB files) :
Chime: Great Sites. (MDL Information Systems, Inc.)
MolUSc - Molecules pour un Usage Scholaire: (French )
Cross-indexing terms: protein explorer, simplified; surfaces; sequence to structure; comparison of 2 molecules; French.
MolUSc is a Chime-based web resource in French (MolUSc is the French acronym for Molecules for Scholarly Use). It may be thought of as a simpler Protein Explorer. Its aim is to give students full access to Chime possibilities, without needing to know any RasMol script commands.
In MolUSc all commands are available in easy-access menus. MolUSc allows surface displays, selections from sequences, comparing two molecules... MolUSc works with Netscape Navigator and even better in Internet Explorer. MolUSc can be downloaded and used freely for non commercial purposes.
MolUSc est un programme de manipulation de molecules base sur le plug-in Chime (MolUSc signifie modelisation de Molecules pour un Usage Scolaire). L'objectif de MolUSc est de donner l'acces aux eleves a toutes les possibilites de Chime, au travers d'une interface conviviale, sans avoir a taper d'instructions de commande. MolUSc permet d'afficher des surfaces, de faire des selections a partir des sequences, de comparer deux molecules,... MolUSc fonctionne avec Netscape Navigator mais aussi avec Internet Explorer (meme mieux). MolUSc peut etre telecharge, et utilise librement dans un but educatif et non commercial uniquement.
Author: Pillot, Paul Submitted by: the author. (Entry 128). Submitted on Dec 14, 2001.
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: (English, Spanish, German, Portuguese )
is easy to remember for accessing diverse tutorials and molecular visualization resources listed alphabetically elsewhere in this index, such as DNA Structure, Hemoglobin, Antibody, Major Histocompatibility, Lipid Bilayers and Channels, vibrations in IR spectroscopy, simulation of water forming hydrogen bonds, the Protein Explorer, Protein Morpher, Atlas of Macromolecules, Noncovalent Bond Finder, Toobers in Science Education, History of Visualization of Biological Macromolecules, Knots in Proteins, and methods for creating web pages using MDL Chime. One thing that distinguishes from other collections of molecular visualization resources is that all of the tutorials at are downloadable.
Author: Martz, Eric Submitted by: the author. (Entry 154). Submitted on Oct 1, 2004.
Morpher, Protein:
Cross-indexing terms: recoverin, morph; conformational changes, morphs; EF-hand, morph; calmodulin, morphs; influenza hemagglutinin, morph; integrin CD11b MIDAS domain, morph; cAMP kinase, morph; calcium binding to an EF-hand, morph.
At : Morphs of conformational changes, featuring recoverin, a calcium-activated myristoyl switch and its EF-hands binding/losing calcium. Also offered are undocumented morphs of calmodulin binding calcium, then peptide; influenza hemagglutinin low pH change; integrin CD11b MIDAS domain putative affinity increase for ligand; and cAMP kinase binding regulatory peptide. Introduction addresses the purpose of morphing, and the pros and cons of linear interpolation vs. plausible intermediate modeling. Morphing methods are detailed. Downloadable for off-line use, local installation or modification.
Author: Martz, Eric Submitted by: the author. (Entry 54). Submitted on Aug 8, 2000. Last revised on Oct 3, 2004.
most abundant enzyme :
Rubisco: a first look at the mechanism. An experiment in molecular visualisation. (Nixon, John)
mRNA :
Sickle Cell Anemia: Understanding the Molecular Biology. (Sabo, John; Lynch, Jamie; Raineri, Deanna)
mRNA :
Ribosome Tour. (Decatur, Wayne)
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MSA3D :
Protein Explorer, Advanced. (Martz, Eric; (MSA3D component coauthored by Paul Stothard))
MscL, Mechanosensitve Large Conductance Channel (1msl.pdb) :
Membrane Channel & Pump Structures. (McClure, William)
MscS, Mechanosensitve Small Conductance Channel (1mxm.pdb) :
Membrane Channel & Pump Structures. (McClure, William)
MthK K+ Channel (1lnq.pdb) :
Membrane Channel & Pump Structures. (McClure, William)
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Multiple protein sequence alignment coloring :
Protein Explorer, Advanced. (Martz, Eric; (MSA3D component coauthored by Paul Stothard))
multiple sequence alignment :
AHo's Amazing Atlas of Antibody Structure. (Honegger, Annemarie)
multiple sequence alignment coloring of a protein :
ConSurf Server for the Identification of Functional Regions in Proteins by Surface Mapping of Phylogenetic Information. (Glaser, Fabian; Ben-Tal, Nir; Pupko, Tal; Martz, Eric)
multiple structure alignment :
Structural Alignment Program for Proteins. (Gille, Christoph)
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Mustard Gas :
Molecule of the Month/University of Bristol. (May, Paul (editor))
mutant proteins :
Hemoglobin II. (White, Brian)
mutation :
ConSurf Server for the Identification of Functional Regions in Proteins by Surface Mapping of Phylogenetic Information. (Glaser, Fabian; Ben-Tal, Nir; Pupko, Tal; Martz, Eric)
mutations :
Sickle Cell Anemia: Understanding the Molecular Biology. (Sabo, John; Lynch, Jamie; Raineri, Deanna)
mutations :
Structural Alignment Program for Proteins. (Gille, Christoph)
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MutH :
MutH (at The Online Macromolecular Museum). (Carney, Jessica; Silva, Nathan; Marcey, David)
MutH (at The Online Macromolecular Museum):
Cross-indexing terms: mismatch repair; DNA repair; DNA methylation; MutH; MutS; MutL; endonuclease MutH; restiction enzyme, homolog MutH.
The MutH protein of Escherichia coli, a weak endonuclease, is one enzyme of a multimeric complex that works to repair DNA base mismatches (with the exception of C-C pairs) and small insertion or deletion mismatches in strands differing in up to four nucleotides. This Chime-based exhibit explores the structure/function relationships of this DNA repair protein.
Authors: Carney, Jessica; Silva, Nathan; Marcey, David. Submitted by: Marcey, David. (Entry 126). Submitted on Aug 12, 2001.
MutL :
MutH (at The Online Macromolecular Museum). (Carney, Jessica; Silva, Nathan; Marcey, David)
MutS :
MutH (at The Online Macromolecular Museum). (Carney, Jessica; Silva, Nathan; Marcey, David)
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MutS DNA Mismatch Repair Protein :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
MutS DNA Repair Protein (at The Online Macromolecular Museum):
Cross-indexing terms: mismatch repair; DNA repair; DNA methylation; DNA binding.
The MutS protein of E. coli is responsible for repairing mismatched base errors that occur in DNA replication. MutS increases the fidelity of DNA replication 100-1,000 times. This Chime-based exhibit explores the structure-function relationships of MutS.
Authors: Stoffregen, Eric; Marcey, David. Submitted by: Marcey, David. (Entry 101). Submitted on Jun 17, 2001.
MyoD :
Molecules and Structures Homepage. (Gasser, Charles)
myoglobin :
Oxygen Binding Proteins: Myoglobin and Hemoglobin. (Reichsman, Frieda; Driscoll, Timothy)
myoglobin :
Introduction to Protein Structure, Part I. (Bragin, Victoria (Vicki))
myoglobin :
Garrett and Grisham Interactive Biochemistry Structure Tutorials. (Caras, James)
myoglobin :
Molecular Science Lab. (Oberholser, Karl)
myoglobin :
Garrett & Grisham Interactive Biochemistry. (Garrett, R. H.; Grisham, C. M.)
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Myoglobin (oxy) (1mbo.pdb), a monomeric O2 carrier :
Protein Structures List. (McClure, William)
myohemerythrin :
Molecular Science Lab. (Oberholser, Karl)
Myosin :
The Lycoming College Macromolecular Modeling and Bioinformatics Page. (Newman, Jeff)
Myosin :
BioMolecular Explorer 3D: Resources for High School Biology. (Reichsman, Frieda; Eric Martz)
NAD+ :
Molecules for Modern/Cell Biology. (McClure, William)
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NAD+ binding :
Exploring Glyceraldehyde-3-phosphate dehydrogenase. (Bruist, Michael)
NCBI :
XdomView: A Chime-based Graphical Tool for Protein Domain and Exon Position Visualization. (Gopalan, Vivek; Shoba Ranganathan; Tan Tin Wee)
Nef :
HIV-1 Nef Protein (at The Online Macromolecular Museum). (Somple, Maggie; Silva, Nathan; Marcey, David)
NFAT :
Molecules and Structures Homepage. (Gasser, Charles)
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NFKappaB :
Molecules and Structures Homepage. (Gasser, Charles)
nitrite reductase :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
nitrogen metabolism :
Nitrogen Regulatory Protein C (at The Online Macromolecular Museum). (Carroll, Carla; Marcey, David)
Nitrogen Regulatory Protein :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
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Nitrogen Regulatory Protein C (at The Online Macromolecular Museum):
Cross-indexing terms: transcription factor; nitrogen metabolism; phosphorylation, protein; NtrC.
Nitrogen Regulatory Protein C (NtrC) is a positively acting bacterial transcription factor that is involved in regulating the metabolism of nitrogen. This exhibit explores the structure-function relationships of the N-terminal receiver domain of NtrC. Special attention is paid to the conformational changes of the receiver domain induced by phosphorylation.
Authors: Carroll, Carla; Marcey, David. Submitted by: Marcey, David. (Entry 113). Submitted on Jun 18, 2001.
nitrogenase :
Chime Square. (Niederhoffer, Eric)
Nitrous oxide :
Molecule of the Month/University of Bristol. (May, Paul (editor))
NMR :
Course Home Page for "Computer Applications in Biotechnology". (Klevickis, Cindy)
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NMR ensembles played as movie :
Protein Explorer, Advanced. (Martz, Eric; (MSA3D component coauthored by Paul Stothard))
Noncovalent Bond Finder :
Protein Explorer, Advanced. (Martz, Eric; (MSA3D component coauthored by Paul Stothard))
NonCovalent Bond Finder (NCBF):
Cross-indexing terms: hydrogen bonds, finding; hydrophobic interactions, finding; van der Waals interactions, finding; salt bridges, finding.
At : The NonCovalent Bond Finder is a Chime-based tool for finding and displaying the atoms closest to any moiety of interest ("target") in any molecule. After loading your molecule and selecting the target atom or atoms, simply pressing a button labeled "Find" displays the atoms within 2.5 Angstroms of the target. Repeated presses of the "Find" button move out in 0.1 Angstrom increments, highlighting newly found atoms with dot surfaces. The starting distance and step size are configurable. The "find only" and "don't find" options enable, for example, only hydrogen bonds, or only hydrophobic interactions to be visualized in a given cycle. A detailed tutorial is provided, using the binding of a nonapeptide to a major histocompatibility protein as an example. Here is a snapshot of the NCBF in action. Downloadable for off-line use, local installation or modification.
Author: Martz, Eric Submitted by: the author. (Entry 55). Submitted on Aug 8, 2000. Last revised on Oct 3, 2004.
noncovalent bonds :
Chemical Bonds and Protein Structure (at The Online Macromolecular Museum). (Marcey, David)
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Noncovalent Interactions in Proteins:
Cross-indexing terms: noncovalent interactions in proteins; ligand-protein complexes; pi-orbital interactions; cation-pi interactions; aromatic sidechains: face-to-face, side-to-face, face-to-cation; salt bridges.
A Chime-based web page dedicated to the importance and prevalence of pi-type interactions in proteins and protein-ligand complexes. Specific noncovalent interactions are shown that stabilize the structure of protein systems. A special emphasis has been placed on pi-type interactions such as cation-pi interactions between aromatic and basic amino-acid side chains and face-to-face and face-to-edge interactions between two aromatic side chains. All the interactions shown were found by biochemistry students who participated in molecular visualization class projects.
Author: Cox, Ricky Submitted by: the author. (Entry 45). Submitted on Jul 17, 2000.
Noncovalent Interactions in Proteins:
Cross-indexing terms: noncovalent interactions in proteins; ligand-protein complexes; pi-orbital interactions; cation-pi interactions; aromatic sidechains: face-to-face, side-to-face, face-to-cation; salt bridges.
A Chime-based web page dedicated to the importance and prevalence of pi-type interactions in proteins and protein-ligand complexes. Specific noncovalent interactions are shown that stabilize the structure of protein systems. A special emphasis has been placed on pi-type interactions such as cation-pi interactions between aromatic and basic amino-acid side chains and face-to-face and face-to-edge interactions between two aromatic side chains. All the interactions shown were found by biochemistry students who participated in molecular visualization class projects.
Author: Cox, Ricky Submitted by: the author. (Entry 45). Submitted on Jul 17, 2000.
NS3 protease :
Biomolecules at Kenyon College. (Students, Kenyon College; Site Director, Joan Slonczewski) (English; CopG auf Deutch)
NtrC :
Nitrogen Regulatory Protein C (at The Online Macromolecular Museum). (Carroll, Carla; Marcey, David)
nuclear hormone receptor :
Retinoid X Receptor, Human. (Palaga, Tanapat)
nuclear hormone receptor :
Estrogen Receptor Structures & Function. (McClure, Will; Saha, Suparna)
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Nucleic Acid Structure Tutorials:
Cross-indexing terms: DNA, A, B, and Z forms; RNA; DNA-protein interactions; RNA protein interactions; catalytic RNA; ribozymes; homeodomain proteins; tRNA; nucleosome.
Chime-based tutorials of the following structures:Comparison of A, B, and Z DNA. Side-by-side comparison of structures, highlighting stacking, grooves, and base-pairs. Based on Science 216: 475-485.[Medline Abstract]
tRNA structure Highlights tertiary interacions and base-stacking of tRNA. Based on Science. 194, 796-806. [Medline Abstract]
Nucleotide numbering help. In case you have trouble keeping up with the atoms of the nucleotide structures.
GroupI intron ribozyme - Full Structure. Catalytic self-splicing RNA. Includes new tertiary interactions: adenosine platform, the tetraloop receptor,the adenosine platform, the ribose zipper, and the tight turn. Based on Science282:259-264 [Medline abstract]
Hammerhead Ribozyme. Small catalytic RNA, showing conserved residues, U-turn motif near active site. Based on Nature 372, 68-74.[Medline Abstract]
MATa1/alpha2-DNA Complex Shows DNA bending, protein-protein interaction, protein-DNA contacts, water mediated H-bonds. Based on Science 270, 262-269. [Medline abstract]
Nucleosome core particle. Shows the "histone fold", which holds protein core together and interacts with DNA. Non sequence-specific protein-DNA interactions.Based on Nature. 389, 251-60.[Medline abstract].
U1A Protein-RNA structure RNP-domain binding to RNA. Major groove binding at end of RNA helix. Induced fit. Based on Nature. 372, 432-438.[Medline abstract]
Author: Nolan, Jim Submitted by: the author. (Entry 51). Submitted on Jul 21, 2000. Last revised on Dec 4, 2000.
nucleic acids :
DNA Structure. (Reichsman, Frieda) (English, Italian)
nucleic acids :
Chime Square. (Niederhoffer, Eric)
nucleic acids :
Garrett and Grisham Interactive Biochemistry Structure Tutorials. (Caras, James)
nucleic acids :
Garrett & Grisham Interactive Biochemistry. (Garrett, R. H.; Grisham, C. M.)
nucleophilic substitution :
Hammerhead Ribozyme. (Reichsman, Frieda)
Nucleosome :
Structures for Molecular Biology. (McClure, William)
Nucleosome :
Nucleic Acid Structure Tutorials. (Nolan, Jim)
Nucleosome :
Biomodel. (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish)
Nucleosome :
Molecules and Structures Homepage. (Gasser, Charles)
Nucleosome :
BioMolecular Explorer 3D: Resources for High School Biology. (Reichsman, Frieda; Eric Martz)
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nucleotide :
DNA Structure (at The Online Macromolecular Museum). (Marcey, David)
Nucleotide Identification Quiz:
Cross-indexing terms: lesson plan; quiz; nucleotides.
Quiz in a frames format; the user is required to identify 15 common nucleotides shown as Chime images by name and abbreviation. Answers are provided after each selection, and a running total of correct and incorrect responses is tabulated.
Author: McClure, William Submitted by: the author. (Entry 29). Submitted on Jun 1, 2000.
nucleotides :
Nucleotide Identification Quiz. (McClure, William)
nucleotides :
Course Home Page for "Computer Applications in Biotechnology". (Klevickis, Cindy)
nucleotides :
Biomolecular Structures. (Hansson, Orjan)
Nucleotides: A, C, G, T, & U :
Molecules for Modern/Cell Biology. (McClure, William)
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NUS :
XdomView: A Chime-based Graphical Tool for Protein Domain and Exon Position Visualization. (Gopalan, Vivek; Shoba Ranganathan; Tan Tin Wee)
OMPF :
Porin Proteins (at The Online Macromolecular Museum). (Flammer, Kristin; Downs, Aaron; Marcey, David)
oncogene product, ras :
Ras Oncogene Product. (Gorga, Frank)
Online Macromolecular Museum:
Cross-indexing terms: Amino Acid Structures; Protein Structure and Chemical Bonds; DNA Structure; Protein Secondary Structure; Extracellular Matrix Components; Fibronectin; HhaI DNA Methylase; Methylase, DNA; Hin Recombinase; Recombinase; HIV-1 Integrase; HIV-1 Protease; RecA (E. coli); Topoisomerase I; polymerases, DNA; DNA polymerases; HIV Reverse Transcriptase; Reverse Transcriptase, HIV; Phage T7 DNA Replication Complex; Eukaryotic DNA Polymerase Beta; Proliferating cell nuclear antigen (PCNA); Antibody Recognition of Antigen; Immunoglobulin Structure; Viral Antigens; E. coli Porins: OMPF and Maltoporin (LamB); Porins; Catalase; Spliceosomal Protein-RNA Interactions, U1A; Signal Recognition Particle Core (E. coli); Protein Tyrosine Phosphatase; Nitrogen Regulatory Protein; MutS DNA Mismatch Repair Protein; BamHI endonuclease; Tryptophan Repressor; cro repressor; lambda repressor.
|The Online Macromolecular Museum (OMM) is a site for the display and study of macromolecules. The OMM's exhibits are interactive, Chime-based |
|tutorials on individual molecules in which hypertextual explanations of important biochemical features are linked to illustrative renderings of the |
|molecule at hand. The OMM's exhibits are grouped into "halls" based on function. |
|- Hall of Introductory Exhibits |- Hall of DNA Polymerization |- Hall of Ribonucleoproteins |
|- Hall of Catalysis |- Hall of DNA Recombination, Modification, Repair|- Hall of Immunology |
|- Hall of Cell Adhesion | |- Hall of Virology |
|- Hall of Membrane Biology |- Hall of Signal Transduction and Transcription | |
Authors: Marcey, David; Students at California Lutheran University; Students at Kenyon College. Submitted by: the author. (Entry 18). Submitted on Jun 1, 2000. Last revised on Jun 17, 2001.
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operator :
The E. coli trp Repressor Chime Movie. (Lawson, Cathy)
operator DNA :
Cro Repressor of Temperate Bacteriophages (at The Online Macromolecular Museum). (Marcey, David)
organic chemistry :
Web-Based Chemical Investigations. (Bragin, Victoria (Vicki))
organic chemistry sites :
Chime: Great Sites. (MDL Information Systems, Inc.)
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Overviews of DNA & RNA Structure:
Cross-indexing terms: DNA (1bna.pdb); RNA (RNA.pdb).
Side-by-side Chime displays of DNA and RNA with highlighted G-C and A-T(A-U) base pairs.
Author: McClure, William Submitted by: the author. (Entry 25). Submitted on Jun 1, 2000.
oxidative phosphorylation :
Chime Square. (Niederhoffer, Eric)
oxidative stress :
Chime Square. (Niederhoffer, Eric)
oxidoreductase :
Catalase (at The Online Macromolecular Museum). (Boon, Elizabeth; Downs, Aaron; Marcey, David)
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oxygen binding pocket :
Cytochrome P450 3D structures page. (Nelson, David)
Oxygen Binding Proteins: Myoglobin and Hemoglobin:
Cross-indexing terms: myoglobin; hemoglobin; 2,3-bisphosphoglycerate (BPG); sickle cell anemia.
Chime-based tutorial including basics of myoglobin structure and function, interactions with heme, detailed look at hemoglobin's conformational changes with emphasis on the mechanism of R to T state conformational switching. Also includes interaction of hemoglobin with the allosteric regulator BPG, and exploration of sickle cell disease hemoglobin. References to figures in Lehninger's Principles of Biochemistry (Lehninger, Nelson & Cox), 3rd edition. Implementation includes pop-up detail boxes, movies, color keys, extensive help, busy/idle status indicators, and a powerful interface for self-directed exploration of the tutorial images.
Authors: Reichsman, Frieda; Driscoll, Timothy. Submitted by: Driscoll, Timothy. (Entry 33). Submitted on Jun 3, 2000. Last revised on Jun 15, 2000.
oxygenase :
Rubisco: a first look at the mechanism. An experiment in molecular visualisation. (Nixon, John)
oxyhemoglobin :
Animations on subjects of Structural and Metabolic Biochemistry. (Silva, Pedro)
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oxytocin :
Side-by-Side Amino Acid Viewer. (McClure, William)
Ozone :
Molecule of the Month/University of Bristol. (May, Paul (editor))
p21 :
Ras Oncogene Product. (Gorga, Frank)
P450cam :
Cytochrome P450 3D structures page. (Nelson, David)
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PDB :
XdomView: A Chime-based Graphical Tool for Protein Domain and Exon Position Visualization. (Gopalan, Vivek; Shoba Ranganathan; Tan Tin Wee)
PDB Lite:
Cross-indexing terms: Searching for molecules; Molecules, finding.
Designed for novices, students, educators, and occasional users, this search interface to the Protein Data Bank has direct links for viewing molecules in "FirstGlance in Chime" and Protein Explorer. PDB Lite's database is updated weekly with new releases. TheProtein Data Bank is the international archive of all published 3D macromolecular structures.
Authors: Martz, Eric; Prilusky, Jaime. Submitted by: the author. (Entry 38). Submitted on Jun 15, 2000.
peptide bond :
Protein Architecture at Biochemistry in 3D. (Driscoll, Timothy; Reichsman, Frieda)
peptide bond :
Introduction to Protein Structure, Part I. (Bragin, Victoria (Vicki))
peptide bond synthesis :
Ribosome Tour. (Decatur, Wayne)
peptide bond synthesis :
Large Ribosomal Subunit Tour. (Decatur, Wayne)
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peptide structure :
Introduction to Protein Structure. (Gorga, Frank)
peptides :
Biomodel. (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish)
peptides :
Biomolecular Structures. (Hansson, Orjan)
peptides and peptide bond :
Side-by-Side Amino Acid Viewer. (McClure, William)
PERF motif :
Cytochrome P450 3D structures page. (Nelson, David)
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periodic table of the elements :
3D Periodic Table of Radii. (Wherland, Scot)
peroxidase :
Protein Structure Analysis Using Internet Tools: A Tutorial Using Peroxidase. (Rojas, Nina Rosario L.; Quiambao, Paul Rosby M.)
Phage T7 DNA Replication Complex :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
phosphatidyl choline :
Lipid Bilayers and the Gramicidin Channel. (Martz, Eric; Herraez, Angel)
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phosphodiester linkage :
DNA Structure (at The Online Macromolecular Museum). (Marcey, David)
phosphofructokinase :
The Glycolytic Cycle. (Warren, L. Van)
phosphoglucoisomerase :
The Glycolytic Cycle. (Warren, L. Van)
phosphoglycerate kinase :
The Glycolytic Cycle. (Warren, L. Van)
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phosphoglycerate mutase :
The Glycolytic Cycle. (Warren, L. Van)
Phospholipid :
Molecules for Modern/Cell Biology. (McClure, William)
phospholipid bilayers :
Lipid Bilayers and the Gramicidin Channel. (Martz, Eric; Herraez, Angel)
phosphorylation :
Protein Kinase CKII. (Glover III, Claiborne)
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phosphorylation, protein :
Nitrogen Regulatory Protein C (at The Online Macromolecular Museum). (Carroll, Carla; Marcey, David)
phosphorylation/dephosphorylation of proteins :
Protein Tyrosine Phosphatase PTP1B (at The Online Macromolecular Museum). (Silva, Nathan; Marcey, David)
photosynthesis :
Chime Square. (Niederhoffer, Eric)
photosynthesis :
Rubisco: a first look at the mechanism. An experiment in molecular visualisation. (Nixon, John)
photosynthetic reaction center :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
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Photosynthetic Reaction Center (1qov.pdb), the bacterial electron pumping complex :
Protein Structures List. (McClure, William)
pi-orbital interactions :
Noncovalent Interactions in Proteins. (Cox, Ricky)
PKG motif :
Cytochrome P450 3D structures page. (Nelson, David)
polB :
DNA Polymerase Beta (at The Online Macromolecular Museum). (Fries, David; Marcey, David)
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polymerase, DNA :
DNA Polymerase Beta (at The Online Macromolecular Museum). (Fries, David; Marcey, David)
polymerases, DNA :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
polymerization mechanism :
DNA Polymerase I from Thermus aquaticus. (Bruist, Michael)
polypeptide :
Introduction to Protein Structure, Part I. (Bragin, Victoria (Vicki))
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Polythiophene :
Molecule of the Month/University of Bristol. (May, Paul (editor))
porin :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
Porin Proteins (at The Online Macromolecular Museum):
Cross-indexing terms: OMPF; Maltoporin; LamB Porin; Porins; lambda receptor.
The porin superfamily contains a number of homotrimeric, transmembrane proteins that form water-filled pores across the outer cell membranes of gram-negative bacteria. Porins allow bacterial cells to interact with their environment through the passive diffusion of small, hydrophillic solutes across bacterial membranes. OMPF (outer membrane protein f) is among the most general E. coli porins. Maltoporin, also known as the LamB porin, is among the best studied examples of the substrate-specific porins. It is responsible for the guided diffusion of maltose and maltodextrins. Maltoporin is also one of the many porins that contains a bacteriophage recognition sequence. It was identified as the E. coli receptor for phage lambda before its role in the translocation of sugar was discovered. This Chime-based exhibit explores the structure-function relationships of OMPF and Maltoporin.
Authors: Flammer, Kristin; Downs, Aaron; Marcey, David. Submitted by: Marcey, David. (Entry 99). Submitted on Jun 17, 2001.
Porins :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
Porins :
Porin Proteins (at The Online Macromolecular Museum). (Flammer, Kristin; Downs, Aaron; Marcey, David)
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Prealbumin (1eta.pdb), (a.k.a. transerythrin), an antiparallel β-barrel :
Protein Structures List. (McClure, William)
Presentation in Protein Explorer (PIPE - prototype) :
SV40 capsid structure and assembly. (Welte, Stefan)
Presentation in Protein Explorer (PIPE - prototype) :
FtsZ, a prokaryotic cell-division protein and tubulin homologue. (McCool, Gabriel J.)
presentations in Protein Explorer :
Retinoid X Receptor, Human. (Palaga, Tanapat)
primary structure :
Introduction to Protein Structure, Part I. (Bragin, Victoria (Vicki))
primary structure :
Introduction to Protein Structure. (Gorga, Frank)
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primer :
DNA Polymerase I from Thermus aquaticus. (Bruist, Michael)
processivity subunit :
DNA Polymerase III-Beta Subunit (at The Online Macromolecular Museum). (Marcey, David)
Proliferating cell nuclear antigen (PCNA) :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
Proline :
Molecule of the Month/University of Bristol. (May, Paul (editor))
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protease :
BioMolecular Explorer 3D: Resources for High School Biology. (Reichsman, Frieda; Eric Martz)
protease inhibitor :
The Rational Basis of Drug Design. (Walters, D. Eric)
protease inhibitor :
BioMolecular Explorer 3D: Resources for High School Biology. (Reichsman, Frieda; Eric Martz)
protease, HIV-1 :
HIV-1 Protease (at The Online Macromolecular Museum). (Mana, Miyeko; Marcey, David)
proteasome :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
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protein :
XdomView: A Chime-based Graphical Tool for Protein Domain and Exon Position Visualization. (Gopalan, Vivek; Shoba Ranganathan; Tan Tin Wee)
protein architecture :
Protein Secondary Structure, versions 1.0, 2.0, 3.0. (Reichsman, Frieda; Driscoll, Tim)
Protein Architecture at Biochemistry in 3D:
Cross-indexing terms: amino acids; peptide bond; secondary structure; tertiary structure; supersecondary motifs; domains, protein; quaternary structure; Lehninger's Principles of Biochemistry.
Chime-based tutorial including amino acids (stereochemistry, sidechains and categories, proline vs. structure), peptide bond, sequence, secondary structure (phi/psi angles, alpha helices, beta sheets, turns), hydrogen bonds, tertiary structure (fibrous proteins - kinesin, collagen, silk fibroin), small globular proteins (myoglobin, lysozyme), supersecondary motifs, domains, SCOP, examples of alpha, beta, alpha/beta (mixed or segregated), quaternary structure (hemoglobin, poliovirus, tobacco mosaic virus, binding interfaces). References to figures in Lehninger's Principles of Biochemistry (Lehninger, Nelson & Cox), 3rd edition. Implementation includes color keys, extensive help, and busy/idle status indicators.
Authors: Driscoll, Timothy; Reichsman, Frieda. Submitted by: the author. (Entry 1). Submitted on May 24, 2000. Last revised on Jun 15, 2000.
protein C :
Structural Biochemistry of Blood Coagulation. (Walters, D. Eric)
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Protein Explorer for Novices:
Cross-indexing terms: RasMol-like exploration; Chime made easy to use; QuickViews and FirstView; Explorer, Protein; Sequence, clickable, mapping to structure; Seq3D.
Choose any molecule, and explore it in Chime. Protein Explorer makes the power of Chime easy to use. The initial molecular image is maximally informative, and is explained for novices by the FirstView screen. The QuickViews menus and buttons enable powerful visualization by novices without use of RasMol-style commands (but Protein Explorer accepts all RasMol commands should you know any). Every operation is explained with color keys where appropriate. Much easier to use yet more powerful than RasMol, Protein Explorer includes MENU options for selection by chain, rendering of surfaces and contact surfaces, hiding portions of the structure, automated tools for distinguishing DNA from RNA, centering, and coloring by ATCGU or hydrophobicity/polarity. The amino acid or nucleotide sequence can be clicked to locate residues in the 3D structure (Seq3D). Snapshots offer a quick preview. See also Advanced Protein Explorer which has many more capabilities. Downloadable for off-line use, local installation or modification.
Author: Martz, Eric Submitted by: the author. (Entry 36). Submitted on Jun 15, 2000. Last revised on Jul 1, 2002.
Protein Explorer, Advanced:
Cross-indexing terms: Advanced Protein Explorer; Noncovalent Bond Finder; Multiple protein sequence alignment coloring; MSA3D; Contact surfaces; NMR ensembles played as movie.
Choose any molecule, and explore it in Chime. Protein Explorer makes advanced capabilities of Chime easy to use. The Contact Surfaces form produces overviews of noncovalent bonds at interfaces, which can be rendered as solid or transparent surfaces. Cation-pi interactions and salt bridges can be displayed. The Noncovalent Bond Finder makes easy a detailed exploration of hydrogen bonds, hydrophobic interactions, and water bridges. Ensembles of models (as from NMR or morphs) can be played as a movie with custom rendering and coloring. Molecules can be colored to indicate conservation or mutation frequency based on multiple protein sequence alignments (MSA3D). A nonvolatile "expert" preference setting bypasses help for novices.See the Snapshots. See also Protein Explorer for Novices. Downloadable for off-line use, local installation or modification.
Authors: Martz, Eric; (MSA3D component coauthored by Paul Stothard). Submitted by: the author. (Entry 37). Submitted on Jun 15, 2000. Last revised on Aug 11, 2000.
protein explorer, simplified :
MolUSc - Molecules pour un Usage Scholaire. (Pillot, Paul) (French)
Protein G :
Protein Secondary Structure, versions 1.0, 2.0, 3.0. (Reichsman, Frieda; Driscoll, Tim)
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Protein G (1pgb.pdb), crystal structure :
Protein G Structure Tutorial. (McClure, William)
Protein G (2gb1.pdb), NMR structure :
Protein G Structure Tutorial. (McClure, William)
Protein G Structure Tutorial:
Cross-indexing terms: Protein G (1pgb.pdb), crystal structure; Protein G (2gb1.pdb), NMR structure.
In a frames format, the B1 domain of protein G from Streptococcus is used to highlight several features of protein architecture that are found in many other proteins. In addition, each of the Chime images and the buttons that modify them serve as starting points for making changes in the displays.
Author: McClure, William Submitted by: the author. (Entry 22). Submitted on Jun 1, 2000.
protein kinase :
Protein Kinase CKII. (Glover III, Claiborne)
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Protein Kinase CKII:
Cross-indexing terms: casein kinase II; protein kinase; phosphorylation; kinase, protein.
A series of Chime-based tutorials illustrating the structure and function of casein kinase II (CKII), a highly conserved member of the S/T/Y protein kinase family. The three tutorials in the series are designed to be viewed sequentially and address
1. the alpha subunit monomer (maize)
2. the beta subunit dimer (human)
3. the holoenzyme tetramer (human)
Each tutorial consists of a narrative description accompanied by integrated Chime animations that illustrate the major points. The animations, intitated by clicking buttons, can be viewed with minimal viewer interaction, but the user can also manipulate the structures via the Chime pop-up menu. (Note: The stereo mode has been set to cross-eyed rather than default wall-eyed to facilitate viewing in stereo on screen).
Author: Glover III, Claiborne Submitted by: the author. (Entry 131). Submitted on Jun 4, 2002.
Protein Secondary Structure :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
Protein Secondary Structure :
The Zinc Finger: A Protein Domain that Binds Specific DNA Sequences. (Bruist, Michael)
Protein Secondary Structure, versions 1.0, 2.0, 3.0:
Cross-indexing terms: alpha helix; beta sheet; Protein G; protein architecture; hydrogen bonds.
Chime presentations of fundamental folding patterns of proteins, the alpha helix and beta sheet. Emphasis is on understanding why polypeptide chains fold in these patterns, and how these secondary structures fit into proteins. Versions 2.0 and 3.0 are self-paced tutorials with textual explanations for each movie button. Version 3.0 features extensive hyperlinked definitions and explanations, enabling viewers to control the depth of the tutorial. Version 1.0 is designed for instructor use in a lecture format, is implemented with movie buttons that are labelled by key words only, and includes brief sections on the eye-catching Green Fluorescent Protein, others. All include brief Chime Help section.
Authors: Reichsman, Frieda; Driscoll, Tim. Submitted by: the author. (Entry 35). Submitted on Jun 3, 2000.
protein structure :
Carboxypeptidase A - Three Exercises with Chime. (Morgan, Eleanor; Helmerhorst, Erik)
protein structure :
Introduction to Protein Structure. (Gorga, Frank)
protein structure :
Biomolecular Structures. (Hansson, Orjan)
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Protein Structure Analysis Using Internet Tools: A Tutorial Using Peroxidase:
Cross-indexing terms: peroxidase; horseradish peroxidase; databases on-line.
This resource uses Chime to demonstrate the uses of a selection of online protein databases and resources to look at the structure of peroxidases. Among the databases that are introduced are: The Protein Data Bank, SCOP, CATH, FSSP, SAS, 3D-SEARCH.
Authors: Rojas, Nina Rosario L.; Quiambao, Paul Rosby M.. Submitted by: the author. (Entry 76). Submitted on Nov 9, 2000.
Protein Structure and Chemical Bonds :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
Protein Structures List:
Cross-indexing terms: Rubredoxin (1caa.pdb), a small protein consisting mostly of β-meanders; Prealbumin (1eta.pdb), (a.k.a. transerythrin), an antiparallel β-barrel; Triose Phosphate Isomerase (1ypi.pdb), a parallel β-barrel with alternating βαβ motifs; Collagen (1a89.pdb), a theoretical model of the triple helix; α-lactalbumin (1b90.pdb), a human plasma transport protein; Myoglobin (oxy) (1mbo.pdb), a monomeric O2 carrier; Hemoglobin (oxy) (1hho.pdb), the red blood cell O2 carrier; Hemoglobin(deoxy) (1b86.pdb), with bound 2,3-bisphosphoglycerate (BPG); Tropomyosin (2tma.pdb), a fibrous coiled-coil protein; Rop Protein Dimer (1rop.pdb), a globular coiled-coil protein; Immunoglobulin G (Igg.pdb), an all-β antibody protein; Concanavalin A (2cna.pdb), an antiparallel β-barrel; Pyruvate Kinase (1pkn.pdb), a multi-domain protein with three discrete β-structures; Lactate Dehydrogenase (1ldm.pdb), a two-domain protein with a nucleotide-binding motif; Silk Protein (2slk.pdb), a theoretical model of the fibrous β-sheet protein; Bacteriorhodopsin (Br.pdb), a light-driven proton pump; K+-Channel (1bl8.pdb), an ion-selective pore; Maltoporin (2mpr.pdb), a trimeric sugar transporter in bacteria; Hemolysin (7ahl.pdb), a heptameric channel-forming toxin; Photosynthetic Reaction Center (1qov.pdb), the bacterial electron pumping complex.
An index page of links to one-page Chime displays of the structures shown in Chapter 4 of Campbell (and many other biochemistry textbooks). The corresponding figure (or page) numbers are shown. Each page illustrates an important structural feature or general principle found in other proteins. The emphasis here is on the overall architecture of proteins rather than specific functions of individual amino acid residues (more on this topic later!). Mastery of the key principles is required for the course.
Author: McClure, William Submitted by: the author. (Entry 21). Submitted on Jun 1, 2000.
protein superposition :
Structural Alignment Program for Proteins. (Gille, Christoph)
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protein synthesis :
70S Ribosome Architecture. (McClure, Will)
protein synthesis :
The Large Ribosomal Subunit: a structure/function tutorial. (Sontum, Stephen; Lesko, Zack)
protein targeting :
Signal Recognition Particle Core (at The Online Macromolecular Museum). (Marcey, David)
Protein Tyrosine Phosphatase :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
Protein Tyrosine Phosphatase PTP1B (at The Online Macromolecular Museum):
Cross-indexing terms: phosphorylation/dephosphorylation of proteins; tyrosine phosphatases.
The phosphorylation status of a protein can modulate its function, and Protein Tyrosine Kinases (PTKs) and Protein Tyrosine Phosphatases (PTPs) work to regulate protein function in response to a variety of signals, including hormones, mitogens, and growth factors. This Chime-based exhibit focuses on recent structural work on PTP1B, a well studied non-receptor PTP. A homology model of a recently discovered FERM-PTP (Pez) is also discussed.
Authors: Silva, Nathan; Marcey, David. Submitted by: Marcey, David. (Entry 112). Submitted on Jun 18, 2001. Last revised on Jun 19, 2001.
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Protein/DNA interactions:
Cross-indexing terms: 434 repressor; trp repressor; Met J repressor; zinc fingers; leucine zippers; EcoRI.
This web resource uses Chime to illustrate one of the final year modules of a biochemistry course covering Protein/DNA interactions. The pages have been written with education in mind, and there is also a "Chime Trainer Page" developed alongside the web pages designed to train students in the use of Chime. The user interface incorporates buttons within frames to create a walkthrough tutorial effect for each of the specific DNA/Protein interactions that are covered.From the initial page the chime resources can be found by navigating through the links to lectures with Chime tutorials, and then scrolling to the bottom of these pages where a button to open the chime tutorial can be found.
Authors: Gibson, Andrew; Sims, P. F. G.. Submitted by: the author. (Entry 58). Submitted on Aug 15, 2000.
proteins :
Biomodel. (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish)
Psilocybin :
Molecule of the Month/University of Bristol. (May, Paul (editor))
Ptaquiloside :
Molecule of the Month/University of Bristol. (May, Paul (editor))
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pymol :
Structural Alignment Program for Proteins. (Gille, Christoph)
pyrophosphate :
Isoprenoid Biosynthesis Pathway. (Warren, L. Van)
pyruvate :
The Glycolytic Cycle. (Warren, L. Van)
pyruvate kinase :
The Glycolytic Cycle. (Warren, L. Van)
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Pyruvate Kinase (1pkn.pdb), a multi-domain protein with three discrete β-structures :
Protein Structures List. (McClure, William)
quarternary structure :
Introduction to Protein Structure. (Gorga, Frank)
quaternary structure :
Protein Architecture at Biochemistry in 3D. (Driscoll, Timothy; Reichsman, Frieda)
quaternary structure :
Introduction to Protein Structure, Part I. (Bragin, Victoria (Vicki))
quaternary structure :
Exploring Glyceraldehyde-3-phosphate dehydrogenase. (Bruist, Michael)
quercetin :
Interactive Quercetin 2,3-Dioxygenase Presentation. (Pijning, T)
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QuickViews and FirstView :
Protein Explorer for Novices. (Martz, Eric)
quiz :
Amino Acid Identification Quiz. (McClure, William)
quiz :
Nucleotide Identification Quiz. (McClure, William)
quiz question interface :
Carboxypeptidase A - Three Exercises with Chime. (Morgan, Eleanor; Helmerhorst, Erik)
quiz, amino acid structure :
Amino Acid Structure Quiz. (McClure, William)
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quizzer, amino acid :
Amino Acid Quizzer. (Martz, Eric; White, Brian)
quizzer, DNA :
DNA quizzer. (White, Brian)
quizzes using Chime displays and GIF images :
Molecular Models for Biochemistry at CMU. (McClure, William)
Ras Oncogene Product:
Cross-indexing terms: oncogene product, ras; conformational changes in ras oncogene product; G protein, low molecular weight; p21; guanine nucleotide binding protein.
This CHIME enhanced presentation is targeted at advanced undergraduate students taking courses in Biochemistry or Cell Biology. This presentation introduces oncogenes and biological signal transduction before turning to ras as an example of a molecular switch. The two conformations of RAS are displayed using CHIME and the user can easily switch between them. Lastly the structural basis for the two classes of oncogenic ras mutants (i.e. those affecting GTPase activity and those affecting nucleotide affinity) are discussed.
Author: Gorga, Frank Submitted by: the author. (Entry 88). Submitted on Mar 8, 2001.
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RasMol :
Macromolecular Visualization Laboratory Exercise. (Kahn, Kalju)
RasMol :
Structural Alignment Program for Proteins. (Gille, Christoph)
RasMol-like exploration :
Protein Explorer for Novices. (Martz, Eric)
RBE :
Biomodel. (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish)
reading frames :
Sickle Cell Anemia: Understanding the Molecular Biology. (Sabo, John; Lynch, Jamie; Raineri, Deanna)
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real time animation :
Rubisco: a first look at the mechanism. An experiment in molecular visualisation. (Nixon, John)
RecA (E. coli) :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
RecA Protein (at The Online Macromolecular Museum):
Cross-indexing terms: DNA recombination; SOS response; LexA protease; DNA, single stranded; DNA; Holliday Junction; DNA recombination.
The RecA protein of E. coli is a critical enzyme in DNA recombination, as it catalyzes the pairing of single-stranded DNA with complementary regions of double stranded DNA. In addition to its role in homologous recombination, RecA functions as a coprotease for the LexA protein during the SOS response. This Chime-based exhibit explores the structure-function relationships of this complex enzyme.
Authors: Heerssen, Heather; Downs, Aaron; Marcey, David. Submitted by: Marcey, David. (Entry 103). Submitted on Jun 17, 2001.
receptor binding :
Erythropoietin - EPO Receptor Complex (at The Online Macromolecular Museum). (Marcey, David)
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recombinant DNA technology :
Restriction Enzymes: Eco RV. (Reichsman, Frieda)
Recombinase :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
Recombinase :
Hin Recombinase (at The Online Macromolecular Museum). (Millard, Elizabeth; Downs, Aaron; Marcey, David)
recoverin, morph :
Morpher, Protein. (Martz, Eric)
Redox Proteins:
Cross-indexing terms: cytochromes; iron-sulfur proteins; copper proteins; lesson plan.
Redox Proteins is an Internet tutorial intended as a computer-based laboratory exercise for undergraduate students in biochemistry. It covers organic redox cofactors, redox enzymes with organic cofactors, cytochromes, iron-sulfur proteins, copper proteins, complexes of redox proteins and multisubunit redox proteins. The tutorial makes use of the Chemscape Chime plug-in and JavaScript. Particular attention has been paid to the design of the user interface so that students which are not so experienced with computers can navigate easily through the tutorial. A form with simple questions is included. Extensive help is available to guide the user.
Author: Hansson, Orjan Submitted by: the author. (Entry 133). Submitted on Jun 7, 2002.
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repressor :
The E. coli trp Repressor Chime Movie. (Lawson, Cathy)
repressors :
Chime Square. (Niederhoffer, Eric)
residue annotation :
Structural Alignment Program for Proteins. (Gille, Christoph)
respiratory chain complexers :
Animations on subjects of Structural and Metabolic Biochemistry. (Silva, Pedro)
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restiction enzyme, homolog MutH :
MutH (at The Online Macromolecular Museum). (Carney, Jessica; Silva, Nathan; Marcey, David)
restriction enzymes :
BamHI Restriction Endonuclease (at The Online Macromolecular Museum). (Silva, Nathan; Leslie, Kenneth; Marcey, David)
Restriction Enzymes: Eco RV:
Cross-indexing terms: cloning; endonuclease; recombinant DNA technology; genetic engineering.
Eco RV is used to explain the fundamental principles of restriction enzyme action on double-stranded DNA. Domain structure, specific and non-specific binding to DNA, bending of DNA, and catalytic site structure are emphasized. Smooth transitions between views show their relationships clearly. The interface is easy to use for students and novices, but advanced users can modify the images with menus, or enter Chime commands.
Author: Reichsman, Frieda Submitted by: the author. (Entry 93). Submitted on Jun 5, 2001.
Retinoid X Receptor, Human:
Cross-indexing terms: nuclear hormone receptor; presentations in Protein Explorer.
This presentation is focusing on the basic structure of human retinoid X receptor and the conformational changes upon ligand binding. The presentation starts with the unliganded form of the receptor and ends with the liganded and unliganded forms aligned in one image.
This presentation is in the Protein Explorer (v.1.72 beta) using Chime. It is a prototype of this presentation mode. From any image in the presentation, you can move into Explorer to change the display, color scheme, hide portions and zoom, etc., then return to the presentation.
Author: Palaga, Tanapat Submitted by: the author. (Entry 86). Submitted on Feb 6, 2001.
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retroviral Nef :
HIV-1 Nef Protein (at The Online Macromolecular Museum). (Somple, Maggie; Silva, Nathan; Marcey, David)
retroviral protease :
HIV-1 Protease (at The Online Macromolecular Museum). (Mana, Miyeko; Marcey, David)
retrovirus :
HIV-1 Reverse Transcriptase (at The Online Macromolecular Museum). (Goldman, Matthew; Marcey, David)
Rev protein :
Biomodel. (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish)
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reverse transcriptase and non-nucleoside inhibitors thereof :
HIV-1 Reverse Transcriptase (at The Online Macromolecular Museum). (Goldman, Matthew; Marcey, David)
Reverse Transcriptase, HIV :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
RGD :
Fibronectin (at The Online Macromolecular Museum). (Ward, Michael; Marcey, David)
rhinovirus :
Macromolecular Visualization Laboratory Exercise. (Kahn, Kalju)
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ribbon :
Introduction to Protein Structure, Part I. (Bragin, Victoria (Vicki))
Ribosomal small subunit :
The Lycoming College Macromolecular Modeling and Bioinformatics Page. (Newman, Jeff)
ribosome :
The Large Ribosomal Subunit: a structure/function tutorial. (Sontum, Stephen; Lesko, Zack)
ribosome structure and translation :
70S Ribosome Architecture. (McClure, Will)
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Ribosome Tour:
Cross-indexing terms: RNA, ribosomal; translation; peptide bond synthesis; tRNA; mRNA; 30S ribosomal subunit; 70S Ribosome architecture; 50S ribosomal subunit.
An introductory tour of the ribosome suitable for high school or college general biology classes. Includes the two RNA subunits, numerous proteins, 3 transfer RNAs, and messenger RNA. Based on the first structure for the complete ribosome, reported in May, 2001, by Noller and coworkers.
Author: Decatur, Wayne Submitted by: the author. (Entry 120). Submitted on Jun 20, 2001. Last revised on Nov 7, 2003.
ribosome, large subunit :
Large Ribosomal Subunit Tour. (Decatur, Wayne)
ribosome, large subunit for specialists :
Large Ribosomal Subunit Tour for Specialists. (Decatur, Wayne)
ribozyme :
Large Ribosomal Subunit Tour for Specialists. (Decatur, Wayne)
ribozyme :
Hammerhead Ribozyme. (Reichsman, Frieda)
ribozyme :
Large Ribosomal Subunit Tour. (Decatur, Wayne)
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ribozymes :
Nucleic Acid Structure Tutorials. (Nolan, Jim)
ribulose-1,5-bisphosphate carboxylase :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
ritonavir :
The Rational Basis of Drug Design. (Walters, D. Eric)
RNA :
Nucleic Acid Structure Tutorials. (Nolan, Jim)
RNA :
Biomodel. (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish)
RNA :
Hammerhead Ribozyme. (Reichsman, Frieda)
RNA :
Biomolecular Structures. (Hansson, Orjan)
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RNA (RNA.pdb) :
Overviews of DNA & RNA Structure. (McClure, William)
RNA enzyme :
Hammerhead Ribozyme. (Reichsman, Frieda)
RNA protein interactions :
Nucleic Acid Structure Tutorials. (Nolan, Jim)
RNA splicing :
U1A Spliceosomal Protein (at The Online Macromolecular Museum). (Marcey, David)
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RNA, ribosomal :
Large Ribosomal Subunit Tour for Specialists. (Decatur, Wayne)
RNA, ribosomal :
Ribosome Tour. (Decatur, Wayne)
RNA, ribosomal :
Large Ribosomal Subunit Tour. (Decatur, Wayne)
role of water as reactant :
Rubisco: a first look at the mechanism. An experiment in molecular visualisation. (Nixon, John)
Rop Protein Dimer (1rop.pdb), a globular coiled-coil protein :
Protein Structures List. (McClure, William)
rRNA :
Large Ribosomal Subunit Tour for Specialists. (Decatur, Wayne)
rRNA :
Biomodel. (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish)
rRNA :
Large Ribosomal Subunit Tour. (Decatur, Wayne)
rRNA :
The Large Ribosomal Subunit: a structure/function tutorial. (Sontum, Stephen; Lesko, Zack)
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rubisco :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
rubisco :
Rubisco: a first look at the mechanism. An experiment in molecular visualisation. (Nixon, John)
Rubisco: a first look at the mechanism. An experiment in molecular visualisation.:
Cross-indexing terms: Innovative framing approach to CHIME based tutorials; mage; Schreudr.kin; photosynthesis; carbon fixation; genetic engineering; Rubisco; structure and mechanism; RuBP as substrate; role of water as reactant; carboxylase; oxygenase; beta-elimination; coordination at metal site; carbamate; stereoelectronic control; access to the active site; most abundant enzyme; enzyme kinetics; slowest enzyme; real time animation; timing of active site closure; hyperthermophilic archaeon; thermophilic red alga..
'Rubisco: a first look at the mechanism' is an experiment in molecular visualisation using an innovative framing approach to CHIME based tutorials. Exploring the mechanism of 'the world's most abundant enzyme', throws light on why the Rubisco is also one of the slowest enzymes (turnover rate of 3 /sec). After consulting the excellent Chime demonstration of the structure of Rubisco and having a look at Schreudr.kin, you begin an interactive Chime tutorial. The tutorial looks in detail at: changes to the substrate RuBP; activation of Rubisco; coordination at the metal site; loop 6 and the N-terminus of neighbouring L chain; changes round the P1 and P2 sites; access to the active site; the contribution of loop 6; access to the active site; the neighbouring L subunit; the reason for isolating the active site? the timing of active site closure; the role of the small subunit S and other issues. A formulation of the mechanism outlined in the publications of I. Andersson et al (e.g.J. Mol. Biol. 259, 160-174) is compared with the formulation published in Cleland et al (Chem. Rev. 98, 549-561). The tutorial, which requires substantial time, was originally written under the auspices of PPS99. Constructive feedback is welcome. The tutorial works either with Netscape 4 or IE6 and Chime 2.6 SP4.
Author: Nixon, John Submitted by: the author. (Entry 69). Submitted on Oct 2, 2000. Last revised on Aug 12, 2004.
RuBP as substrate :
Rubisco: a first look at the mechanism. An experiment in molecular visualisation. (Nixon, John)
Rubredoxin (1caa.pdb), a small protein consisting mostly of β-meanders :
Protein Structures List. (McClure, William)
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rybozymes :
Biomodel. (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish)
saccharin :
Everything You Ever Wanted to Know about Sweeteners. (Walters, D. Eric)
Saint John's wort :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
Salbutamol :
Molecule of the Month/University of Bristol. (May, Paul (editor))
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salt bridges :
Noncovalent Interactions in Proteins. (Cox, Ricky)
salt bridges :
Chemical Bonds and Protein Structure (at The Online Macromolecular Museum). (Marcey, David)
salt bridges, finding :
NonCovalent Bond Finder (NCBF). (Martz, Eric)
salt-briges :
Magnesium Adenosine Triphosphate (MgATP) Binding to an Enzyme. (Bruist, Michael)
saquinavir :
The Rational Basis of Drug Design. (Walters, D. Eric)
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Sarin, cubane :
Molecule of the Month/University of Bristol. (May, Paul (editor))
Saxitoxin :
Molecule of the Month/University of Bristol. (May, Paul (editor))
Schreudr.kin :
Rubisco: a first look at the mechanism. An experiment in molecular visualisation. (Nixon, John)
SCOP :
XdomView: A Chime-based Graphical Tool for Protein Domain and Exon Position Visualization. (Gopalan, Vivek; Shoba Ranganathan; Tan Tin Wee)
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scripting methods in Chime :
How to Create New Chime Tutorials. (Martz, Eric)
Searching for molecules :
PDB Lite. (Martz, Eric; Prilusky, Jaime)
secondary structure :
Protein Architecture at Biochemistry in 3D. (Driscoll, Timothy; Reichsman, Frieda)
secondary structure :
Introduction to Protein Structure, Part I. (Bragin, Victoria (Vicki))
secondary structure :
Garrett and Grisham Interactive Biochemistry Structure Tutorials. (Caras, James)
secondary structure :
Introduction to Protein Structure. (Gorga, Frank)
secondary structure :
Garrett & Grisham Interactive Biochemistry. (Garrett, R. H.; Grisham, C. M.)
Seq3D :
Protein Explorer for Novices. (Martz, Eric)
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sequence to structure :
MolUSc - Molecules pour un Usage Scholaire. (Pillot, Paul) (French)
sequence variability :
AHo's Amazing Atlas of Antibody Structure. (Honegger, Annemarie)
Sequence, clickable, mapping to structure :
Protein Explorer for Novices. (Martz, Eric)
SERCA1 Ca2+ Pump (1eul.pdb, 1iwo.pdb) :
Membrane Channel & Pump Structures. (McClure, William)
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serine esterase :
Molecular Science Lab. (Oberholser, Karl)
Serum Response Factor (SRF) :
Molecules and Structures Homepage. (Gasser, Charles)
SGI workstations :
Macromolecular Visualization Laboratory Exercise. (Kahn, Kalju)
SH3 domain interaction :
HIV-1 Nef Protein (at The Online Macromolecular Museum). (Somple, Maggie; Silva, Nathan; Marcey, David)
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sickle cell anemia :
Oxygen Binding Proteins: Myoglobin and Hemoglobin. (Reichsman, Frieda; Driscoll, Timothy)
sickle cell anemia, point mutation :
Hemoglobin-S Polymerization Binding Site. (Howard, Vince)
Sickle Cell Anemia: Understanding the Molecular Biology:
Cross-indexing terms: mRNA; introns; exons; DNA; base pairing; amino acids; transcription; translation; mutations; stop codons; reading frames; hemoglobin; disease.
This tutorial was created in order to demonstrate how a single nucleotide substitution in one of the beta-globin chains of human hemoglobin leads to the disease, sickle cell anemia. The Biology Workbench is used to align a "normal" or "wildtype" beta-globin sequence with a mutated or sickle cell sequence to show the location of the mutation. The Protein Explorer program is then used to identify the affected amino acid in the beta-globin protein chain and to visualize how the mutation changes the structure and conformation of the hemoglobin molecule. Chime version 2.0.3 is needed on PCs and version 2.0a for Macs.
Authors: Sabo, John; Lynch, Jamie; Raineri, Deanna. Submitted by: Raineri, Deanna. (Entry 75). Submitted on Nov 9, 2000. Last revised on Mar 25, 2001.
sickle hemoglobin :
Hemoglobin. (Martz, Eric)
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sickle-cell anemia :
Hemoglobin II. (White, Brian)
Side-by-Side Amino Acid Viewer:
Cross-indexing terms: amino acids, all 20; Met-enkephalin; oxytocin; peptides and peptide bond.
In a frames format, the selection forms above each frame let you view each of the 20 amino acids using the Chemscape Chime Plug-in. The buttons in each frame highlight side chain functional groups, overall dimensions, and side chain polarity. The last six entries in the selection lists are peptides. In addition to highlighting features of the peptide bond, these models serve as a review of amino acid side-chain structures.
Author: McClure, William Submitted by: the author. (Entry 20). Submitted on Jun 1, 2000.
side-chain interactions :
Hemoglobin I. (White, Brian)
sidechain :
Introduction to Protein Structure, Part I. (Bragin, Victoria (Vicki))
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signal recognition :
Signal Recognition Particle Core (at The Online Macromolecular Museum). (Marcey, David)
Signal Recognition Particle:
Cross-indexing terms: SRP, the E. coli signal recognition particle, (1dul.pdb); E. coli Ffh protein: the protein subunit without RNA (2ffh.pdb); Domain IV RNA Structure (1cq5.pdb)..
A one-page Chime display of the signal recognition particle (SRP) shows the M domain of E. coli Ffh protein complexed with domain IV of 4.5S RNA (1dul.pdb). There are also links to similar Chime displays of:
Domain IV RNA Structure: the average NMR structure of the RNA alone (1cq5.pdb).
Ffh protein: the protein subunit without RNA (2ffh.pdb).
All three models in a side-by-side display on one page.
Author: McClure, William Submitted by: the author. (Entry 23). Submitted on Jun 1, 2000. Last revised on Jun 3, 2000.
Signal Recognition Particle Core (at The Online Macromolecular Museum):
Cross-indexing terms: signal recognition; protein targeting; SRP.
In both eukaryotes and prokaryotes, a signal recognition particle (SRP) is responsible for recognizing and binding to a signal sequence at the amino terminus of a growing, membrane-bound protein. This is essential for targeting the protein to the membrane. This exhibit focuses on the structure of the SRP core of E. coli, which represents an evolutionarily preserved core of the SRP in all organisms.
Author: Marcey, David Submitted by: the author. (Entry 114). Submitted on Jun 18, 2001.
Signal Recognition Particle Core (E. coli) :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
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sildenafil :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
sildenafil :
The Rational Basis of Drug Design. (Walters, D. Eric)
Silk Protein (2slk.pdb), a theoretical model of the fibrous β-sheet protein :
Protein Structures List. (McClure, William)
simulation, theoretical, water :
Water Simulation. (Martz, Eric)
Singapore :
XdomView: A Chime-based Graphical Tool for Protein Domain and Exon Position Visualization. (Gopalan, Vivek; Shoba Ranganathan; Tan Tin Wee)
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Sliding DNA clamp :
DNA Polymerase III-Beta Subunit (at The Online Macromolecular Museum). (Marcey, David)
slowest enzyme :
Rubisco: a first look at the mechanism. An experiment in molecular visualisation. (Nixon, John)
Small Molecule Lab Exercise:
Cross-indexing terms: amino acid quizzer; lab exercise.
In the first page, students are given a few simple structures to draw from the chime image. This familiarizes them with the interface & the representation used by chime. In the second page, they randomly select amino acids by number from a protein and must identify them by structure.
Author: White, Brian Submitted by: the author. (Entry 80). Submitted on Nov 10, 2000.
small molecules :
Molecular Visualization Resources for Project VISM. (Klevickis, Cindy)
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SN1 reaction :
DNA Polymerase I from Thermus aquaticus. (Bruist, Michael)
snRNP :
U1A Spliceosomal Protein (at The Online Macromolecular Museum). (Marcey, David)
snRNP U1A :
Structures for Molecular Biology. (McClure, William)
solvent accessible surface :
Accessible, molecular and Van der Waals surfaces explained. (Krieger, Elmar)
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SOS response :
RecA Protein (at The Online Macromolecular Museum). (Heerssen, Heather; Downs, Aaron; Marcey, David)
SP1 :
Molecules and Structures Homepage. (Gasser, Charles)
spermine :
Course Home Page for "Computer Applications in Biotechnology". (Klevickis, Cindy)
Spliceosomal Protein-RNA Interactions, U1A :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
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spliceosome :
Biomodel. (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish)
Splicesomal Protein :
U1A Spliceosomal Protein (at The Online Macromolecular Museum). (Marcey, David)
Squalene :
Isoprenoid Biosynthesis Pathway. (Warren, L. Van)
src-family :
Explore the c-Src tyrosine kinase. (Engen, John R; Superti-Furga, Giulio)
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SRP :
Signal Recognition Particle Core (at The Online Macromolecular Museum). (Marcey, David)
SRP, the E. coli signal recognition particle, (1dul.pdb) :
Signal Recognition Particle. (McClure, William)
Staurosporine :
Molecule of the Month/University of Bristol. (May, Paul (editor))
stem-loop :
Hammerhead Ribozyme. (Reichsman, Frieda)
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stereoelectronic control :
Rubisco: a first look at the mechanism. An experiment in molecular visualisation. (Nixon, John)
stereoisomerism :
Web-Based Chemical Investigations. (Bragin, Victoria (Vicki))
Steroids :
Isoprenoid Biosynthesis Pathway. (Warren, L. Van)
stop codons :
Sickle Cell Anemia: Understanding the Molecular Biology. (Sabo, John; Lynch, Jamie; Raineri, Deanna)
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Structural Alignment Program for Proteins:
Cross-indexing terms: alignment; protein superposition; pymol; jmol; rasmol; vmd; mutations; residue annotation; java; multiple structure alignment.
STRAP is an interactive editor for multiple sequence alignments of proteins. Several tutorials and wizards on the following topics are integrated in STRAP:
1. mapping of mutations and polymorphisms onto three-dimensional protein structures
2. multiple structure alignments
3. BLAST searches
4. evolutionary dendrograms
5. multiple sequence alignments of sequences with little similarity
These tutorials are the basis for training courses which are offered for students of biophysics, biochemistry and biology at the Humboldt University Berlin
Author: Gille, Christoph Submitted by: the author. (Entry 158). Submitted on Oct 27, 2004.
Structural Biochemistry of Blood Coagulation:
Cross-indexing terms: blood coagulation; tissue factor; factor II; factor III; factor VII; factor IX; factor XIII; von Willebrand factor; protein C; thrombin; hirudin; fibrin.
The structures of many blood coagulation factors have been determined experimentally by X-ray crystallography or by NMR spectroscopy. These pages illustrate structural features of these proteins using Chime. Included are tissue factor (factor III); a tissue factor + factor VII complex; von Willebrand factor; tissue factor pathway inhibitor; protein C; a portion of factor IX containing several gamma-carboxy-glutamate residues; thrombin (factor II, complexed with hirudin, a leech anticoagulant); factor XIII; a fibrin fragment.
Author: Walters, D. Eric Submitted by: the author. (Entry 73). Submitted on Nov 6, 2000.
structural domain :
XdomView: A Chime-based Graphical Tool for Protein Domain and Exon Position Visualization. (Gopalan, Vivek; Shoba Ranganathan; Tan Tin Wee)
structure and mechanism :
Rubisco: a first look at the mechanism. An experiment in molecular visualisation. (Nixon, John)
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structure, protein, primary, secondary :
Introduction to Protein Structure, Part I. (Bragin, Victoria (Vicki))
structure-activity relationships :
The Rational Basis of Drug Design. (Walters, D. Eric)
Structures for Molecular Biology:
Cross-indexing terms: B-Form DNA helix; A-Form RNA helix; cAMP Receptor Protein (CRP); Yeast GAL4 Protein; Human hnRNP A1; snRNP U1A; EF-Tu, tRNAPhe, and GTP; Zif268 zinc finger; EcoRI Res. Endonuclease; HhaI Res. Methylase; Nucleosome.
An index table of structures for molecular biology courses. PubMed entries and Chime displays of the structures can be viewed by following the links provided.
Author: McClure, William Submitted by: the author. (Entry 27). Submitted on Jun 1, 2000.
strucuture :
XdomView: A Chime-based Graphical Tool for Protein Domain and Exon Position Visualization. (Gopalan, Vivek; Shoba Ranganathan; Tan Tin Wee)
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Student Webpapers: The Structure-Function Relationships for the Enzymes in the Glycolytic and Lactate Fermentation Pathways.:
Cross-indexing terms: glycolysis; gluconeogenesis; lactate fermentation; Classroom use of Chime; lesson plan.
Students taking Chem406 at the University of Wisconsin-Eau Claire are required to write a Web termpaper (Webpaper) that reviews the structure-function relationships of a protein. Chem406 is a biophysical chemistry course that is required of undergraduate students majoring in Biochemistry/Molecular Biology. For the Fall 1999 semester the students were assigned enzymes from the glycolytic, gluconeogenesis, and lactate fermentation pathways. The students were required to use Chime images to illustrate their papers and to use JavaScript buttons to modify these images in context with the narrative of their paper. We have found Web page authoring with Chimes to be a powerful tool for teaching students about the structure/function relationships of proteins. The homepage for this site contains two links: one to the detailed assignment that was given to the students, the other to a figure showing the metabolic pathways involved. Each enzyme named in this figure provides a link to a student Webpaper. These are student-authored reports, unedited by faculty, consequently the quality and accuracy does vary. All together there are 12 Webpapers with a average of three Chimes per Webpaper. The specific enzymes covered include:
• Hexokinase (E.C.2.7.1.1)
• Glucose 6-Phosphate Isomerase (E.C.5.3.1.9)
• Phosphofructokinase (E.C.2.7.1.11)
• Fructose 1,6-Bisphosphate Aldolase (E.C. 4.1.2.13)
• Triosephosphate Isomerase (E.C. 5.3.1.1)
• Glyceraldehyde 3-Phosphate Dehydrogenase (E.C. 1.2.1.12)
• 3-Phosphoglycerate Kinase (E.C. 2.7.2.3)
• 3-Phosphoglycerate Mutase (E.C. 5.4.2.1)
• 2-Phosphoglycerate Hydrolase (Enolase) (E.C. 4.2.1.11)
• Pyruvate Kinase (E.C. 2.7.1.40)
• Fructose 1,6-Bisphosphatase (E.C. 3.1.3.11)
• Lactate Dehydrogenase (E.C. 1.1.1.27)
Author: Chem406 Class, Fall 1999, U Wisc-Eau Claire Submitted by: Gallagher, Warren. (Entry 57). Submitted on Aug 10, 2000.
student-authored tutorials :
Course Home Page for "Computer Applications in Biotechnology". (Klevickis, Cindy)
substrate binding :
Magnesium Adenosine Triphosphate (MgATP) Binding to an Enzyme. (Bruist, Michael)
succinate dehydrogenase :
Animations on subjects of Structural and Metabolic Biochemistry. (Silva, Pedro)
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sucralose :
Everything You Ever Wanted to Know about Sweeteners. (Walters, D. Eric)
Sucrose -> Fructose & Glucose :
Molecules for Modern/Cell Biology. (McClure, William)
Sulfanilamide :
Molecule of the Month/University of Bristol. (May, Paul (editor))
supersecondary motifs :
Protein Architecture at Biochemistry in 3D. (Driscoll, Timothy; Reichsman, Frieda)
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surfaces :
MolUSc - Molecules pour un Usage Scholaire. (Pillot, Paul) (French)
surfaces :
Accessible, molecular and Van der Waals surfaces explained. (Krieger, Elmar)
SV40 capsid structure and assembly.:
Cross-indexing terms: Presentation in Protein Explorer (PIPE - prototype); VP1; virus capsid structure; icosahedral capsid structure.
The major component of the Simian Virus 40 capsid is 360 copies of VP1. This is a detailed tour of how VP1 fits into pentamers, and how the 72 pentamers assemble to form an icosahedral capsid. It ends with a rotatable 'soccer ball' image of the capsid within an icosahedron. In addition to 30 views in Chime, schematic diagrams are included, and this presentation is a prototype within Protein Explorer 1.0. This means you can use the full capabilities of Protein Explorer to manipulate any view in the presentation. (An earlier version of this SV40 tutorial is available at Univ Massachusetts.)
Author: Welte, Stefan Submitted by: the author. (Entry 7). Submitted on May 25, 2000. Last revised on Dec 16, 2000.
sweetener :
Everything You Ever Wanted to Know about Sweeteners. (Walters, D. Eric)
SYBYL :
Macromolecular Visualization Laboratory Exercise. (Kahn, Kalju)
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Tamoxifen :
Molecule of the Month/University of Bristol. (May, Paul (editor))
TATA box binding protein :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
TATA-binding protein :
Molecules and Structures Homepage. (Gasser, Charles)
Tc3 transposase :
Biomolecules at Kenyon College. (Students, Kenyon College; Site Director, Joan Slonczewski) (English; CopG auf Deutch)
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template :
DNA Polymerase I from Thermus aquaticus. (Bruist, Michael)
tertiary structure :
Protein Architecture at Biochemistry in 3D. (Driscoll, Timothy; Reichsman, Frieda)
tertiary structure :
Introduction to Protein Structure, Part I. (Bragin, Victoria (Vicki))
tertiary structure :
Introduction to Protein Structure. (Gorga, Frank)
Tetrodotoxin :
Molecule of the Month/University of Bristol. (May, Paul (editor))
TFIIIA :
Molecules and Structures Homepage. (Gasser, Charles)
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Thalidomide :
Molecule of the Month/University of Bristol. (May, Paul (editor))
The 20 common amino acids:
Cross-indexing terms: amino acids and properties; lesson plan.
Each amino acid is displayed (with hydrogens) in Chime in a table including names, structural formulae, pI and pK values. A list of questions for a class is provided as a lesson plan (click the separate link "Exploring Amino Acids and Proteins - An Internet Assignment for Biology Students"). Most of the questions can be answered from the table of amino acids, but some extend to electrophoresis, and the uses of other websites to determine isoelectric points of arbitrary peptides, and the use of Entrez to find protein sequences.
Authors: Bragin, Victoria (Vicki); Johnston, Wendie. Submitted by: the author. (Entry 63). Submitted on Aug 17, 2000. Last revised on Mar 19, 2001.
The E. coli trp Repressor Chime Movie:
Cross-indexing terms: trp repressor; trpR; repressor; trp operator; operator; DNA binding protein; ligand activation; tryptophan.
This Chime movie illustrates the structural differences between crystal structures of the inactive apo form (3WRP) and liganded active form (1TRO) of trp repressor, a DNA binding protein from E. coli. Both structures are superimposed in a single PDB file which is downloaded to the left frame. Apo vs. holo forms are selected by toggling push buttons, and the trp operator DNA can also be toggled on and off. The site was designed to make it possible to easily compare these structures, and to illustrate one of few examples where the structural basis for ligand-activation of a DNA-binding protein has been clearly elucidated using crystal structure analysis.
Author: Lawson, Cathy Submitted by: the author. (Entry 68). Submitted on Sep 24, 2000.
The Glycolytic Cycle:
Cross-indexing terms: glucose; hexokinase; ATP; ADP; phosphoglucoisomerase; phosphofructokinase; aldolase; glyceraldehyde-3-phosphate; phosphoglycerate kinase; 3-phosphoglycerate; phosphoglycerate mutase; 2-phosphoglycerate; enolase; 2-phosphoenolpyruvate; pyruvate kinase; pyruvate; lactate dehydrogenase; lactate.
Chime is used to illustrate each step in the glycolytic cycle including the full structure of each substrate and enzyme and the free energy change occurring at each step.
Author: Warren, L. Van Submitted by: the author. (Entry 60). Submitted on Aug 15, 2000.
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The Large Ribosomal Subunit: a structure/function tutorial:
Cross-indexing terms: protein synthesis; enzyme mechanism; translation; rRNA; tRNA; ribosome.
By this point, the ribosome should be a familiar object in your biochemistry/biology education because all life as we know it requires a ribosome to construct proteins. The peptide bond formation it catalyzes is rather simple; however, the complete molecule must also read mRNA codons, and bind 3 tRNA molecules. This accounts, in part, for the large size of the molecule. Unfortunately, much of the mechanism remains a mystery. In a series of papers published in 2000, researchers have determined the structure of the large subunit to a great degree of accuracy, and have proposed specific residues which catalyze the peptide bond formation in large subunit. In this tutorial, we will examine the large subunit, and in doing so, will address three related questions. Which of the components of the large subunit comprise the active site, where is that site located, and how does it work? This tutorial uses the Chime plugin to visualize the three dimensional structure of the ribosome and to animate the mechanism of peptide formation.
Authors: Sontum, Stephen; Lesko, Zack. Submitted by: the author. (Entry 147). Submitted on Feb 12, 2004.
The Lycoming College Macromolecular Modeling and Bioinformatics Page:
Cross-indexing terms: HIV protease; Ribosomal small subunit; Adenosine Kinase; Dystrophin; G-protein Beta and Gamma subunits; DNA glycosylase; Clathrin; Fibronectin; Myosin; Insulin receptor; Dihydrofolate reductase.
The Bioinformatics exercises at Lycoming were designed to use 's Jellyfish software. 3-D protein structure tutorials require the Chime plug-in. The students have produced Integrated Informatics Projects (99-04) and Protein Structure/Function Projects (98-99) that illustrate the structures and functions of many proteins.
Author: Newman, Jeff Submitted by: Foley, Brian. (Entry 159). Submitted on Nov 1, 2004.
The Rational Basis of Drug Design:
Cross-indexing terms: drug discovery; HIV; inhibitor, protease; protease inhibitor; HIV-protease inhibitor; saquinavir; indinavir; ritonavir; sildenafil; Viagra; structure-activity relationships.
Supplementary materials for a series of graduate lectures on the discovery of new drugs. Includes numerous chemical structures and several Chime structures. Illustrated with detailed descriptions of the development of HIV protease inhibitors and the discovery of sildenafil (Viagra).
Author: Walters, D. Eric Submitted by: the author. (Entry 74). Submitted on Nov 6, 2000.
The Zinc Finger: A Protein Domain that Binds Specific DNA Sequences:
Cross-indexing terms: DNA binding protein; zinc finger; zif268; protein secondary structure; lesson plans.
A zinc finger-DNA complex is used to introduce protein structure. Initially, a single finger (without DNA) is viewed. It consists of a beta hairpin and an alpha helix. Various parts of this structure can be viewed separately. The students are asked a few simple questions regarding the structure. Answers are available with a click.
Then, a three-figer structure and the DNA it binds is viewed. Again different parts of the complex can be selected. A few questions are asked of the structure. Answers are provided.
Author: Bruist, Michael Submitted by: the author. (Entry 137). Submitted on Sep 10, 2002.
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theoretical simulation of water :
Water Simulation. (Martz, Eric)
Thermal motion of alpha helix:
Cross-indexing terms: XYZ format animation; animation with XYZ files.
Molecular dynamics simulation of thermal motion of a 12-residue polyalanine right-handed helix unfolding. This illustrates Chime's ability to display animations using XYZ-format atomic coordinate files. Note that unlike PDB files, XYZ files lack information about residue names or atom positions within residues (e.g. alpha carbon). Hence for proteins, NMR-format PDB files are preferable (see the Morpher).
Author: Cachau, Raul E. Submitted by: Martz, Eric. (Entry 53). Submitted on Aug 8, 2000.
thermophilic red alga. :
Rubisco: a first look at the mechanism. An experiment in molecular visualisation. (Nixon, John)
thiolate ligand :
Cytochrome P450 3D structures page. (Nelson, David)
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thrombin :
Structural Biochemistry of Blood Coagulation. (Walters, D. Eric)
timing of active site closure :
Rubisco: a first look at the mechanism. An experiment in molecular visualisation. (Nixon, John)
tissue factor :
Structural Biochemistry of Blood Coagulation. (Walters, D. Eric)
tobacco mosaic virus :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
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Topoisomerase I :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
topoisomerase, type I :
DNA Topoisomerase I (at The Online Macromolecular Museum). (Kysela, David; Marcey, David)
toxoplasmosis :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
transcription :
Sickle Cell Anemia: Understanding the Molecular Biology. (Sabo, John; Lynch, Jamie; Raineri, Deanna)
transcription :
Lac Repressor: Biochemistry in 3D. (Driscoll, Timothy)
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transcription activation :
Estrogen Receptor Structures & Function. (McClure, Will; Saha, Suparna)
transcription activator :
Zinc Binuclear Clusters. (Craig, Paul)
transcription factor :
Nitrogen Regulatory Protein C (at The Online Macromolecular Museum). (Carroll, Carla; Marcey, David)
transcription factor :
Molecules and Structures Homepage. (Gasser, Charles)
transcription factors :
Chime Square. (Niederhoffer, Eric)
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transcription regulation :
Cro Repressor of Temperate Bacteriophages (at The Online Macromolecular Museum). (Marcey, David)
transcriptional regulation :
Lac Repressor: Biochemistry in 3D. (Driscoll, Timothy)
transfer RNA :
Macromolecular Visualization Laboratory Exercise. (Kahn, Kalju)
translation :
Sickle Cell Anemia: Understanding the Molecular Biology. (Sabo, John; Lynch, Jamie; Raineri, Deanna)
translation :
Large Ribosomal Subunit Tour for Specialists. (Decatur, Wayne)
translation :
Ribosome Tour. (Decatur, Wayne)
translation :
Large Ribosomal Subunit Tour. (Decatur, Wayne)
translation :
The Large Ribosomal Subunit: a structure/function tutorial. (Sontum, Stephen; Lesko, Zack)
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translation (animation) and ribosome structure :
70S Ribosome Architecture. (McClure, Will)
transport :
Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)
trends, periodic, in atomic and ionic sizes :
3D Periodic Table of Radii. (Wherland, Scot)
Tricarboxylic acid cycle :
Images of TCA Cycle Intermediates. (McClure, William)
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Triose Phosphate Isomerase (1ypi.pdb), a parallel β-barrel with alternating βαβ motifs :
Protein Structures List. (McClure, William)
tRNA :
Nucleic Acid Structure Tutorials. (Nolan, Jim)
tRNA :
Biomodel. (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish)
tRNA :
Ribosome Tour. (Decatur, Wayne)
tRNA :
The Large Ribosomal Subunit: a structure/function tutorial. (Sontum, Stephen; Lesko, Zack)
tRNA synthetase :
Biomolecules at Kenyon College. (Students, Kenyon College; Site Director, Joan Slonczewski) (English; CopG auf Deutch)
tRNA synthetase :
Macromolecular Visualization Laboratory Exercise. (Kahn, Kalju)
tRNA Tour:
Cross-indexing terms: tRNAPhe (6tna.pdb).
In a frames format, this Chime-based tutorial displays the secondary and tertiary structural features of yeast tRNAPhe. It is designed to complement the description in Saenger, W. (1984) Principles of Nucleic Acid Structure Ch. 15 "tRNA-A Treasury of Stereochemical Information".
Author: McClure, William Submitted by: the author. (Entry 31). Submitted on Jun 1, 2000.
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tRNAPhe (6tna.pdb) :
tRNA Tour. (McClure, William)
Tropomyosin (2tma.pdb), a fibrous coiled-coil protein :
Protein Structures List. (McClure, William)
trp operator :
The E. coli trp Repressor Chime Movie. (Lawson, Cathy)
trp repressor :
Protein/DNA interactions. (Gibson, Andrew; Sims, P. F. G.)
trp repressor :
The E. coli trp Repressor Chime Movie. (Lawson, Cathy)
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trpR :
The E. coli trp Repressor Chime Movie. (Lawson, Cathy)
trypsin inhibitor :
Molecular Science Lab. (Oberholser, Karl)
trypsinogen-BPTI :
Molecular Science Lab. (Oberholser, Karl)
tryptophan :
The E. coli trp Repressor Chime Movie. (Lawson, Cathy)
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Tryptophan Repressor :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
tubulin :
FtsZ, a prokaryotic cell-division protein and tubulin homologue. (McCool, Gabriel J.)
tutorials on molecular structures :
Molecular Models for Biochemistry at CMU. (McClure, William)
Type II restriction endonuclease :
BamHI Restriction Endonuclease (at The Online Macromolecular Museum). (Silva, Nathan; Leslie, Kenneth; Marcey, David)
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tyrosine kinase :
Explore the c-Src tyrosine kinase. (Engen, John R; Superti-Furga, Giulio)
tyrosine phosphatases :
Protein Tyrosine Phosphatase PTP1B (at The Online Macromolecular Museum). (Silva, Nathan; Marcey, David)
U1A :
Biomodel. (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish)
U1A Spliceosomal Protein (at The Online Macromolecular Museum):
Cross-indexing terms: RNA splicing; Splicesomal Protein; snRNP.
This Chime-based exhibit examines the binding of U1A protein to both the U1 snRNA in the U1 snRNP and to the 3' untranslated region of the mRNA that encodes the U1A protein.
Author: Marcey, David Submitted by: the author. (Entry 111). Submitted on Jun 18, 2001. Last revised on Jun 22, 2001.
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universal joint, molecular: flagellar hook :
Flagellar Hook, Bacterial -- A Molecular Universal Joint. (Martz, Eric)
Valence-Shell Electron-Pair Repulsion Theory (VSEPR) :
Web-Based Chemical Investigations. (Bragin, Victoria (Vicki))
Van der Waals forces :
Chemical Bonds and Protein Structure (at The Online Macromolecular Museum). (Marcey, David)
van der Waals interactions, finding :
NonCovalent Bond Finder (NCBF). (Martz, Eric)
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van der Waals surface :
Accessible, molecular and Van der Waals surfaces explained. (Krieger, Elmar)
Viagra :
The Rational Basis of Drug Design. (Walters, D. Eric)
vibrational modes, infrared spectra, animated :
Infrared spectra, animations of vibrational modes. (Motyka, Eric; Lahti, Paul; Lancashire, Robert J.)
Viral Antigens :
Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)
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Viral Antigens (at The Online Macromolecular Museum):
Cross-indexing terms: HIV gp120; influenza hemagglutinin; flu virus; hemagglutinin, influenza.
This Chime-based exhibit concerns the structure/function/variability of two viral spike antigens, hemagglutinin of the human influenza virus, and glycoprotein 120 (gp120) of the human immunodeficiency virus (HIV-1).
Authors: Mazur, Eric; Marcey, David. Submitted by: Marcey, David. (Entry 117). Submitted on Jun 18, 2001.
viral protease :
HIV-1 Protease (at The Online Macromolecular Museum). (Mana, Miyeko; Marcey, David)
virus capsid structure :
SV40 capsid structure and assembly. (Welte, Stefan)
virus peptides, binding to MHC :
Major Histocompatibility Complex. (Martz, Eric)
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vmd :
Structural Alignment Program for Proteins. (Gille, Christoph)
von Willebrand factor :
Structural Biochemistry of Blood Coagulation. (Walters, D. Eric)
VP1 :
SV40 capsid structure and assembly. (Welte, Stefan)
Water :
Molecule of the Month/University of Bristol. (May, Paul (editor))
Water :
BioMolecular Explorer 3D: Resources for High School Biology. (Reichsman, Frieda; Eric Martz)
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Water Simulation:
Cross-indexing terms: theoretical simulation of water; simulation, theoretical, water; lesson plan; Chime.
At : A theoretical simulation (done with MDL Sculpt) of 10 water molecules assembling into a compact, hydrogen-bonded network. Available as saved animations viewable in Chime, and as a morph for Protein Explorer. Ten questions are provided for students about the final hydrogen-bonded droplet.
Author: Martz, Eric Submitted by: the author. (Entry 153). Submitted on Sep 12, 2004. Last revised on Oct 3, 2004.
Watson-Crick base pairing and hydrogen bonding :
DNA Structure. (Martz, Eric) (English, German, Portuguese, Spanish)
Watson-Crick base pairing and hydrogen bonding :
DNA Structure (with Jmol). (Herraez, Angel; Martz, Eric)
Web-Based Chemical Investigations:
Cross-indexing terms: organic chemistry; Valence-Shell Electron-Pair Repulsion Theory (VSEPR); cycloalkanes; isomerism, constitutional; stereoisomerism; lesson plans.
Interactive tutorials in organic chemistry and biochemistry using Chime. Organic chemistry modules include
• Molecular Geometry and the Valence-Shell Electron-Pair Repulsion Theory
• Cycloalkanes: A Structural Study
• Constitutional Isomerism
• Stereoisomerism
Biochemistry modules are listed individually under Bragin in the author index. These tutorials use a discovery-based approach to learning concepts.
Author: Bragin, Victoria (Vicki) Submitted by: the author. (Entry 61). Submitted on Aug 17, 2000. Last revised on Mar 19, 2001.
WXXXR motif :
Cytochrome P450 3D structures page. (Nelson, David)
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XdomView: A Chime-based Graphical Tool for Protein Domain and Exon Position Visualization:
Cross-indexing terms: domain; CATH; SCOP; DALI; FSSP; MMDB; NCBI; ExInt; BLAST; intron; NUS; Singapore; protein; PDB; structural domain; gene; gene evolution; intron evolution; strucuture; 3DEE; exon; intron.
|[pic] |XdomView (Version 2.1) |
|Enlarged image |A Chime-based Graphical Tool for Protein Domain and Exon Position Visualization |
| |XdomView is a chime-based visualization tool that maps the domain boundaries of the |
| |input PDB chain, obtained from protein structure classification databases (CATH, SCOP,|
| |NCBI, 3DEE and DALI) to its tertiary structure. It also runs BLAST2 for the input PDB |
| |chain sequence against all protein sequences in the ExInt* database and maps the |
| |intron positions and phases of aligned search results on the input protein's 3D |
| |structure. Xdom is a useful visualization tool for scientists working on gene and |
| |protein evolution and structural modeling and classification. |
| |Contact Details : |
| |Gopalan Vivek, Dr. Tan Tin Wee, Dr. Shoba Ranganathan |
| |Bioinformatics Centre |
| |Department of Biochemistry |
| |National University of Singapore |
| |*ExInt - Repository of intron positions, phase and protein sequences of all |
| |multi-exonic eukaryotic genes available in GenBank 122. |
Authors: Gopalan, Vivek; Shoba Ranganathan; Tan Tin Wee. Submitted by: the author. (Entry 134). Submitted on Jun 10, 2002.
XYZ files used for infrared vibrations :
Infrared spectra, animations of vibrational modes. (Motyka, Eric; Lahti, Paul; Lancashire, Robert J.)
XYZ format animation :
Thermal motion of alpha helix. (Cachau, Raul E.)
YASARA :
Accessible, molecular and Van der Waals surfaces explained. (Krieger, Elmar)
Top 0 1 2 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
Yeast GAL4 Protein :
Structures for Molecular Biology. (McClure, William)
Z-DNA :
Biomodel. (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish)
Z-DNA :
DNA Conformers (at The Online Macromolecular Museum). (Marcey, David)
Zif :
Molecules and Structures Homepage. (Gasser, Charles)
zif268 :
The Zinc Finger: A Protein Domain that Binds Specific DNA Sequences. (Bruist, Michael)
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Zif268 zinc finger :
Structures for Molecular Biology. (McClure, William)
Zinc Binuclear Clusters:
Cross-indexing terms: transcription activator; zinc finger; BioEditor.
Zinc binuclear clusters are motifs found in transcriptional regulatory proteins in fungi. An early zinc binuclear cluster was originally thought to be similar to previously described zinc fingers, with four cysteines forming a tetrahedral zinc binding site. Subsequent structural studies strated that the zinc binuclear cluster consists of 6 cysteine residues that are bound to two zinc atoms. This documentary includes text, images, sequence and structural data and molecular visualizations to describe representative members of this family. It is presented in the BioEditor software package.
Author: Craig, Paul Submitted by: the author. (Entry 151). Submitted on May 16, 2004.
zinc finger :
Biomodel. (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish)
zinc finger :
The Zinc Finger: A Protein Domain that Binds Specific DNA Sequences. (Bruist, Michael)
zinc finger :
Zinc Binuclear Clusters. (Craig, Paul)
zinc fingers :
Chime Square. (Niederhoffer, Eric)
zinc fingers :
Protein/DNA interactions. (Gibson, Andrew; Sims, P. F. G.)
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Zyban :
Molecule of the Month/University of Bristol. (May, Paul (editor))
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953 total subject cross-indexing terms.
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