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World Index of BioMolecular Visualization Resources

World Index of BioMolecular Visualization Resources

Biochemical Structure Tutorials

Titles Subjects Authors: Detailed Compact HOME

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

2,3-bisphosphoglycerate (BPG) :

Oxygen Binding Proteins: Myoglobin and Hemoglobin. (Reichsman, Frieda; Driscoll, Timothy)

2-phosphoenolpyruvate :

The Glycolytic Cycle. (Warren, L. Van)

2-phosphoglycerate :


3-phosphoglycerate :



30S ribosomal subunit :

Ribosome Tour. (Decatur, Wayne)


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.)





Large Ribosomal Subunit Tour. (Decatur, Wayne)



70S Ribosome architecture :


70S Ribosome architecture :


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)


-Helix & -Sheet in a Small Protein :

Molecules for Modern/Cell Biology. (McClure, William)

-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.

same pageAn 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 . The tutorial requires (and comes with) YASARA View.

Author: Krieger, Elmar Submitted by: the author. (Entry 152). Submitted on Aug 13, 2004.


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 :



acetylcholinesterase mechanism :


acetylcholinesterase- m-(N,N,N-trimethylammonio)trifluoroacetophenone :


acetylcholinesterase-decamethonium :


acetylcholinesterase-tacrine :



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)


Adenosine Triphosphate :

Molecule of the Month/University of Bristol. (May, Paul (editor))

ADP :


Adrenaline :


Advanced Protein Explorer :

Protein Explorer, Advanced. (Martz, Eric; (MSA3D component coauthored by Paul Stothard))


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.)


albumin, serum :

Garrett and Grisham Interactive Biochemistry Structure Tutorials. (Caras, James)

aldolase :


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



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 :


alpha-helix :

Animations on subjects of Structural and Metabolic Biochemistry. (Silva, Pedro)

Alzheimer's :



amino acid :

Molecules and Structures Homepage. (Gasser, Charles)

amino acid chemistry :


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 MolviZ.Org: 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)


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 :


amino acids :

Biomolecular Structures. (Hansson, Orjan)

Amino Acids & Peptides :



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 :


Anatoxin :



animated gifs :

Course Home Page for "Computer Applications in Biotechnology". (Klevickis, Cindy)

animation of translation in the ribosome :


animation with XYZ files :

Thermal motion of alpha helix. (Cachau, Raul E.)

animations :

Lac repressor bending DNA operon. (Martz, Eric)


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 :


antibodies :

AHo's Amazing Atlas of Antibody Structure. (Honegger, Annemarie)


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.

MolviZ.OrgAt : 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 :


Antibody :


Antibody Recognition of Antigen :


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)


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 :



aromatic sidechains: face-to-face, side-to-face, face-to-cation :

Noncovalent Interactions in Proteins. (Cox, Ricky)

ASBMB :

BioMoleculesAlive.Org. (Biochemistry and Molecular Biology, American Society of)

aspartame :


AT base pair :

DNA Structure. (Martz, Eric) (English, German, Portuguese, Spanish)

AT base pair :

DNA Structure (with Jmol). (Herraez, Angel; Martz, Eric)


atomic radii :

3D Periodic Table of Radii. (Wherland, Scot)

ATP :


ATP :


ATP :


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)


B-DNA :


B-DNA :


B-DNA :


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 :


bacterial photosynthesis :



bacteriophage cro :

Cro Repressor of Temperate Bacteriophages (at The Online Macromolecular Museum). (Marcey, David)

bacteriophage repressor :


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)


Bacteriorhodopsin (1c3w.pdb, 1dze.pdb) :


Bacteriorhodopsin (Br.pdb), a light-driven proton pump :


Bacteriorhodopsin: A membrane-spanning protein :


BamHI endonuclease :



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 :


base pairs :

DNA Structure. (Reichsman, Frieda) (English, Italian)

basic biochemistry for undergrads :



Bence-Jones protein REI monomer & dimer :


bending of DNA :


beta barrel :


beta pleats :



beta sheet :

Protein Secondary Structure, versions 1.0, 2.0, 3.0. (Reichsman, Frieda; Driscoll, Tim)

beta sheet :


beta-elimination :


beta-sheet :


beta-sheet :


bilayer, lipid :


bilayer, lipid :

Lipid Bilayers and the Gramicidin Channel. (Martz, Eric; Herraez, Angel)


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

· download the software

· follow our instructions for installing it

2. Pre-selected biomolecules that fit well in a high school biology curriculum

· each molecule is placed in its biological context with a brief description

· each molecule is linked to an interactive 3D display (assuming prior installation of software)

3. Assistance with lesson planning

· each molecule is linked to background information specially selected for HS teachers

4. Access to additional molecules

· 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.


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.

BioMoleculesAlive.Org:

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 :


blood coagulation :

Structural Biochemistry of Blood Coagulation. (Walters, D. Eric)


Boswellic Acid :


Bowen's Reaction Series :

Molecular Visualization Resources for Project VISM. (Klevickis, Cindy)

BPTI :


Bupropion :



C-helix :

Cytochrome P450 3D structures page. (Nelson, David)

calcium binding to an EF-hand, morph :

Morpher, Protein. (Martz, Eric)

calmodulin, morphs :


cAMP :



cAMP kinase, morph :


cAMP Receptor Protein (CRP) :


CAP (cAMP binding protein) & DNA :


carbamate :



carbon fixation :


carboxylase :


Carboxypeptidase :


carboxypeptidase A :



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 :


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)


Catalase :


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 :



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.


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 :


Chime :

Water Simulation. (Martz, Eric)

Chime :


Chime :


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.


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.


chloramphenicol acetyl transferase :


Chlorophyll :


cholera toxin :


Cholesterol :


Cholesterol :


Cholesterol :



chromophore :


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 :



Cisplatin :


Citric acid cycle :

Images of TCA Cycle Intermediates. (McClure, William)

Citric acid cycle :


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 :



cloning :

Restriction Enzymes: Eco RV. (Reichsman, Frieda)

colicin :


collagen :


collagen :


Collagen (1a89.pdb), a theoretical model of the triple helix :



color-coded multiple sequence alignment :


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)


concanavalin a :


Concanavalin A (2cna.pdb), an antiparallel -barrel :


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)


conformational changes in ras oncogene product :

Ras Oncogene Product. (Gorga, Frank)

conformational changes, morphs :


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.


Contact surfaces :

Protein Explorer, Advanced. (Martz, Eric; (MSA3D component coauthored by Paul Stothard))

coordination at metal site :


CopG :


copper :

Interactive Quercetin 2,3-Dioxygenase Presentation. (Pijning, T)


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 :


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.


cupin :


curriculum resources for biochemistry :

BioMoleculesAlive.Org. (Biochemistry and Molecular Biology, American Society of)

cyclamate :


cycloalkanes :

Web-Based Chemical Investigations. (Bragin, Victoria (Vicki))


CYP101 :


CYP2C5 :


cytochrome bc1 :


cytochrome bc1 :


cytochrome c oxidase :


cytochrome c oxidase :



Cytochrome P450 :


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)


DALI :


databases on-line :

Protein Structure Analysis Using Internet Tools: A Tutorial Using Peroxidase. (Rojas, Nina Rosario L.; Quiambao, Paul Rosby M.)

deoxyhemoglobin :


deoxyribonucleic acid, DNA, major groove, minor groove :

B-Form Deoxyribonucleic Acid (DNA). (Bruist, Michael)


deoxyribose :


Desmosterol :


dethiobiotin synthetase :

Magnesium Adenosine Triphosphate (MgATP) Binding to an Enzyme. (Bruist, Michael)

diabetes :



diffusion :


Dihydrofolate reductase :


dioxygen carriers :


dioxygenase :



diphtheria toxin :


disease :


disulfide bond :


disulfide bonds in immunoglobulin :



DNA :


DNA :


DNA :


DNA :


DNA :

RecA Protein (at The Online Macromolecular Museum). (Heerssen, Heather; Downs, Aaron; Marcey, David)

DNA :


DNA :

Macromolecular Visualization Laboratory Exercise. (Kahn, Kalju)

DNA :


DNA & RNA :


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 :


DNA binding :

HhaI DNA Methyltransferase (at The Online Macromolecular Museum). (Douglass, Ben; Downs, Aaron; Marcey, David)


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 :



DNA methylation :


DNA methylation :


DNA methylation :

MutH (at The Online Macromolecular Museum). (Carney, Jessica; Silva, Nathan; Marcey, David)

DNA modification :


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.


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 polymerases :


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.


DNA recombination :


DNA recombination :


DNA recombination :

HIV-1 Integrase (at The Online Macromolecular Museum). (Walsh, Matthew; Marcey, David)

DNA recombination :


DNA repair :


DNA repair :



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 MolviZ.Org: 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.


DNA Structure :


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 Structure :


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.


DNA substrate :


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)


DNA, A, B, and Z forms :


DNA, single stranded :


DNA-binding :


DNA-binding protein :

BamHI Restriction Endonuclease (at The Online Macromolecular Museum). (Silva, Nathan; Leslie, Kenneth; Marcey, David)


DNA-protein interactions :


domain :


Domain IV RNA Structure (1cq5.pdb). :

Signal Recognition Particle. (McClure, William)

domains :



domains, protein :

Protein Architecture at Biochemistry in 3D. (Driscoll, Timothy; Reichsman, Frieda)

double helix :


double helix, DNA :


double helix, DNA :


drug discovery :

The Rational Basis of Drug Design. (Walters, D. Eric)


Dystrophin :


E. coli Ffh protein: the protein subunit without RNA (2ffh.pdb) :

Signal Recognition Particle. (McClure, William)

E. coli Glycerol Channel (1fx8.pdb, 1ldi.pdb) :


E. coli Porins: OMPF and Maltoporin (LamB) :



EcClC Chloride Channel (1ots.pdb, 1otu.pdb) :


EcoRI :

Protein/DNA interactions. (Gibson, Andrew; Sims, P. F. G.)

EcoRI Res. Endonuclease :


EF-hand, morph :



EF-Tu :


EF-Tu, tRNAPhe, and GTP :


electron transport chain :


electron transport chain :


Elements :



elements, periodic table of :

3D Periodic Table of Radii. (Wherland, Scot)

Enantiomers of glyceraldehyde :


endonuclease :


endonuclease MutH :



Engrailed :


enolase :


enzyme active site :


enzyme kinetics :



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 :


epitopes, T-cell :

Major Histocompatibility Complex. (Martz, Eric)


EPO :


Erythropoietin :


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 ER and ER 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 ER and ER 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.


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.

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 :


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)


ExInt :


exon :


exons :


exonuclease :



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)


Extracellular Matrix Components :


EXXR motif :


factor II :


factor III :



factor IX :


factor VII :


factor XIII :


Farnesyl pyrophosphate :



Fats: Glycerol & Fatty Acids :


Ferritin :


fibrin :


Fibronectin :


Fibronectin :



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 :


Finasteride :


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.


flu virus :

Viral Antigens (at The Online Macromolecular Museum). (Mazur, Eric; Marcey, David)

fluorescence :


Formaldehyde :


Fos :



fosmidomycin :


Frankincense :


French :

MolUSc - Molecules pour un Usage Scholaire. (Pillot, Paul) (French)

FSSP :



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 :


G protein, low molecular weight :


G proteins :



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 :


Gal4 :


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.


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 :


GC base pair :


GCN4 :


gene :



gene evolution :


gene expression :


gene regulation in bacteria :

Lac Repressor: Biochemistry in 3D. (Driscoll, Timothy)

General DNA structure :

Estructura de Macromoleculas. (Sanz, Jesus M.) (Spanish)


General protein structure :

Estructura de Macromoleculas. (Sanz, Jesus M.) (Spanish)

genetic engineering :


genetic engineering :


genetic switch :


Geranyl pyrophosphate :



GFP :


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 :


Glucocorticoid receptor :



gluconeogenesis :


gluconeogenesis :


glucose :


glutamate receptor :


glyceraldehyde-3-phosphate :



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 :


glycolysis :


glycosylation :



glycosylation of antibody, N-linked :


gramicidin channel :


gramicidin channel in lipid bilayer :


green fluorescent protein :



GTP-binding protein FtsZ :

FtsZ, a prokaryotic cell-division protein and tubulin homologue. (McCool, Gabriel J.)

GTP/GDP binding site and induced conformational changes :


guanine nucleotide binding protein :


H-2 (mouse MHC) :

Major Histocompatibility Complex. (Martz, Eric)


H2O cluster :


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 :


helix-turn-helix :



hemagglutinin, influenza :

Viral Antigens (at The Online Macromolecular Museum). (Mazur, Eric; Marcey, David)

Hemoglobin:

Cross-indexing terms: sickle hemoglobin.

MolviZ.OrgAt : 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.


Hemoglobin :


Hemoglobin :

Oxygen Binding Proteins: Myoglobin and Hemoglobin. (Reichsman, Frieda; Driscoll, Timothy)

Hemoglobin :


Hemoglobin :

Hemoglobin-S Polymerization Binding Site. (Howard, Vince)

Hemoglobin :


Hemoglobin :

Hemoglobin I. (White, Brian)

Hemoglobin :

Hemoglobin II. (White, Brian)

Hemoglobin :


Hemoglobin :


Hemoglobin :


Hemog

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