Subject Index

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

(Entry 70). Submitted on Nov 1, 2000.

3D Periodic Table of Radii (using Jmol):

Cross-indexing terms

Atomic and ionic radii in Jmol
Inspired by Scot Wherland's Chime page, redesigned using Jmol and adding some other ideas. Uses Jmol's values of radii (for many more atoms) and Jmol's colors (more specific than Rasmol's).
A version in Spanish is also available.

Author

Herraez, Angel

Submitted by

(Entry 166). Submitted on Feb 15, 2006.

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3DEE :

XdomView: A Chime-based Graphical Tool for Protein Domain and Exon Position Visualization. (Gopalan, Vivek; Shoba Ranganathan; Tan Tin Wee)

3Fe-4S and 4Fe-4S Ferredoxin :

The Guided Tours of Metalloproteins. (Morris, Robert; Lee, Adrian; Hadzovic, Alen)

434 repressor :

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

50S ribosomal subunit :

Ribosome Tour. (Decatur, Wayne)

50S ribosomal subunit :

Large Ribosomal Subunit Tour. (Decatur, Wayne)

50S ribosomal subunit :

70S Ribosome Architecture. (McClure, Will)

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70S Ribosome architecture :

Ribosome Tour. (Decatur, Wayne)

70S Ribosome architecture :

70S Ribosome Architecture. (McClure, Will)

A-DNA :

DNA Conformers (at The Online Macromolecular Museum). (Marcey, David)

A-Form RNA helix :

Structures for Molecular Biology. (McClure, William)

a-Helix & b-Sheet in a Small Protein :

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

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a-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

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

(Entry 152). Submitted on Aug 13, 2004.

acesulfame :

Everything You Ever Wanted to Know about Sweeteners. (Walters, D. Eric)

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Acetyl-CoA :

Isoprenoid Biosynthesis Pathway. (Warren, L. Van)

Aconitase :

The Guided Tours of Metalloproteins. (Morris, Robert; Lee, Adrian; Hadzovic, Alen)

actin polymerization and depolymerization :

Molecular Movies - A Portal to Cell and Molecular Animation. (McGill, Gael; and many others)

actinomycin :

Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)

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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))

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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))

Aequoria victoria :

GFP (Green Fluorescent Protein). (Driscoll, Timothy)

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AHo's Amazing Atlas of Antibody Structure:

Cross-indexing terms

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

(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)

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aldolase :

The Glycolytic Cycle. (Warren, L. Van)

alignment :

Structural Alignment Program for Proteins. (Gille, Christoph)

Alkaline phosphatase:

Cross-indexing terms

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

(Entry 79). Submitted on Nov 10, 2000.

Alkaline phosphatase:

Cross-indexing terms

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

(Entry 79). Submitted on Nov 10, 2000.

Alkohole, Kohlenhydrate, Carbonsaeuren, Aminosaeuren, Eiweisse :

Chemie und Internet am Gymnasium. (Rausch, Martin) (German)

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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 - in English. (Herraez, Angel)

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)

amino acid :

Molecules and Structures Homepage. (Gasser, Charles)

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amino acid chemistry :

Introduction to Protein Structure. (Gorga, Frank)

Amino Acid Identification Quiz:

Cross-indexing terms

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

(Entry 28). Submitted on Jun 1, 2000.

Amino Acid Quizzer:

Cross-indexing terms

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

(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

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

(Entry 149). Submitted on May 16, 2004. Last revised on Nov 26, 2007.

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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 - in English. (Herraez, Angel)

amino acids :

Biomolecular Structures. (Hansson, Orjan)

Amino Acids & Peptides :

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

amino acids and properties :

The 20 common amino acids. (Bragin, Victoria (Vicki))

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amino acids, all 20 :

Side-by-Side Amino Acid Viewer. (McClure, William)

aminoacid :

Prote�nas: aspectos estructurales b�sicos. (Pons, Gabriel) (Spanish)

Anatoxin :

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

animated gifs :

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

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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)

animations of vibrations, infrared spectra :

Infrared spectra, animations of vibrational modes. (Motyka, Eric; Lahti, Paul; Lancashire, Robert J.)

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Animations on subjects of Structural and Metabolic Biochemistry:

Cross-indexing terms

Chime-based tutorials on protein secondary, structure, hemoglobin and electron-transfer complexes. More will eventually follow.

Author

Silva, Pedro

Submitted by

(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)

Antibody:

Cross-indexing terms

At MolviZ.Org: 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

(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)

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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

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

(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)

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APBS :

Molecular Electrostatics with PMV. (Dallakyan, Sargis; Huey, Ruth; Sanner, Michel)

Apoptosis: molecular visualizations on caspases, bcl-2 family and Nf-kappa B: (Spanish, English )

Cross-indexing terms

This page offers Molecular visualizations based on chime and Jmol 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 Bcl2 proteins which control apoptosis. These proteins are located in the cytosol and on the mitochondrial membrane, where they control the exit of protein from matrix to cytosol when apoptosis is fired. General features are presented with special emphasis on interactions between members. Finally, a visualization 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

(Entry 91). Submitted on May 4, 2001. Last revised on May 16, 2008.

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)

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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 :

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)

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atomic radii :

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

atomic radii :

3D Periodic Table of Radii (using Jmol). (Herraez, Angel)

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)

ATP synthesis and hydrolysis :

Molecular Movies - A Portal to Cell and Molecular Animation. (McGill, Gael; and many others)

authoring new Chime websites, methods :

How to Create New Chime Tutorials. (Martz, Eric)

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azt :

HIV-1 Reverse Transcriptase (at The Online Macromolecular Museum). (Goldman, Matthew; Marcey, David)

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

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

(Entry 85). Submitted on Jan 19, 2001.

B-Form DNA helix :

Structures for Molecular Biology. (McClure, William)

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bacterial photosynthesis :

Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)

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

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

(Entry 24). Submitted on Jun 1, 2000.

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bacteriorhodopsin (1brx.pdb) :

Bacteriorhodopsin. (McClure, William)

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)

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BamHI endonuclease :

Online Macromolecular Museum. (Marcey, David; Students at California Lutheran University; Students at Kenyon College)

BamHI Restriction Endonuclease (at The Online Macromolecular Museum):

Cross-indexing terms

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

(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)

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basic biochemistry for undergrads :

Biomolecular Structures. (Hansson, Orjan)

bcl-2 :

Apoptosis: molecular visualizations on caspases, bcl-2 family and Nf-kappa B. (Pons, Gabriel; Gil, Joan) (Spanish, English)

bending of DNA :

Lac repressor bending DNA operon. (Martz, Eric)

beta barrel :

GFP (Green Fluorescent Protein). (Driscoll, Timothy)

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beta pleats :

Introduction to Protein Structure, Part I. (Bragin, Victoria (Vicki))

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 - in English. (Herraez, Angel)

beta-sheet :

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

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bilayer, lipid :

Biomodel - in English. (Herraez, Angel)

bilayer, lipid :

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

bilayer, lipid :

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

BioEditor :

Zinc Binuclear Clusters. (Craig, Paul)

Biomodel - in English:

Cross-indexing terms

Self-guided tutorial, emphasizing 3D-structure and interaction between macromolecules. An English version, using Jmol models, that includes parts of the main Spanish site (which keeps parallel Chime and Jmol versions, and other material). Models are located inside an explanatory web page. Allows both guided tour and user-chosen pathway and action on models. Biomodel-2: a Jmol version of Eric Martz's Rasmol script on bilayer membranes and gramicidin channel. Biomodel-3 is a module addressed to secondary school students, includes sugars, lipids, some vitamins, amino acids, proteins, bases, nucleosides, nucleotides and nucleic acids. Biomodel-4 contains a Jmol version of Eric Martz's DNA Structure tutorial. Water contains a Jmol version of Eric Martz's Water Animation page.

Author

Herraez, Angel

Submitted by

(Entry 89). Submitted on Mar 13, 2001. Last revised on Jan 13, 2007.

BioMolecular Explorer 3D: Resources for High School Biology:

Cross-indexing terms

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:

Links to software for viewing and exploring molecules in 3D
- download the software
- follow our instructions for installing it
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)
Assistance with lesson planning
- each molecule is linked to background information specially selected for HS teachers
Access to additional molecules
- we show you where to find many other biomolecular 3D displays and tutorials

Authors

Reichsman, Frieda; Eric Martz.

Submitted by

(Entry 160). Submitted on Dec 14, 2004.

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Biomolecular Structures:

Cross-indexing terms

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

(Entry 132). Submitted on Jun 7, 2002. Last revised on Jun 7, 2002.

Biomolecules at Kenyon College: (English; CopG auf Deutch )

Cross-indexing terms

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

(Entry 84). Submitted on Jan 4, 2001. Last revised on Jan 9, 2001.

BioMoleculesAlive.Org:

Cross-indexing terms

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

(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)

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blood coagulation :

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

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)

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Bupropion :

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

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)

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cAMP :

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

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)

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carbamate :

Rubisco: a first look at the mechanism. An experiment in molecular visualisation. (Nixon, John)

carbon fixation :

Rubisco: a first look at the mechanism. An experiment in molecular visualisation. (Nixon, John)

Carbonic Anhydrase :

The Guided Tours of Metalloproteins. (Morris, Robert; Lee, Adrian; Hadzovic, Alen)

carboxylase :

Rubisco: a first look at the mechanism. An experiment in molecular visualisation. (Nixon, John)

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Carboxypeptidase :

Carboxypeptidase A - Three Exercises with Chime. (Morgan, Eleanor; Helmerhorst, Erik)

carboxypeptidase A :

Carboxypeptidase A - Three Exercises with Chime. (Morgan, Eleanor; Helmerhorst, Erik)

carboxypeptidase A :

The Guided Tours of Metalloproteins. (Morris, Robert; Lee, Adrian; Hadzovic, Alen)

Carboxypeptidase A - Three Exercises with Chime:

Cross-indexing terms

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

(Entry 47). Submitted on Jul 17, 2000.

carboxypeptidase enzyme :

Carboxypeptidase A - Three Exercises with Chime. (Morgan, Eleanor; Helmerhorst, Erik)

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carnation italian ringspot virus :

RNA Silencing Suppression by a Plant Viral Protein: Structural Basis. (Decatur, Wayne)

casein kinase II :

Protein Kinase CKII. (Glover III, Claiborne)

caspases :

Apoptosis: molecular visualizations on caspases, bcl-2 family and Nf-kappa B. (Pons, Gabriel; Gil, Joan) (Spanish, English)

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

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

(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

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

(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

Lernumgebungen mit CHIME und Skriptsteuerung:

Alkohole
Kohlenhydrate
Carbonsaeuren
Aminosaeuren und Eiweisse

Author

Rausch, Martin

Submitted by

(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 :

Chime and Jmol Files. (Jakubowski, Henry)

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

(Entry 65). Submitted on Aug 22, 2000. Last revised on Aug 22, 2000.

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Chime and Jmol Files:

Cross-indexing terms

The site contains links to interactive Chime and Jmol files that are available from my online book: Biochemistry Online: An Approach Based on Chemical Logic. Some are links to outside files, but most have been created specifically for my Biochemistry I class and for my online. Most of the Chime files have been created by students. For the tutorials we created, the structural coordinates for the molecules were downloaded directly from the Protein Data Bank without further refinements or energy minimizations. In many the PDB files were simplified to show just the protein of interest. These files have been made over a five year period. The earlier ones are less interactive and have contain less written information. These tutorials are generally not sophisticated but get the main structural interest points across. I created the JMol tutorials this summer from the student Chime tutorials and corrected some factual biochemistry errors in some of the students projects.

Author

Jakubowski, Henry

Submitted by

(Entry 167). Submitted on Sep 7, 2006. Last revised on Sep 7, 2006.

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

"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

(Entry 40). Submitted on Jul 8, 2000. Last revised on Jun 12, 2001.

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Chime: Great Sites:

Cross-indexing terms

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

(Entry 9). Submitted on May 25, 2000.

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)

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Cholesterol :

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

Cholesterol :

Isoprenoid Biosynthesis Pathway. (Warren, L. Van)

Cholesterol :

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

Cholesterol :

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

chromatin packing and condensation :

Molecular Movies - A Portal to Cell and Molecular Animation. (McGill, Gael; and many others)

chromophore :

GFP (Green Fluorescent Protein). (Driscoll, Timothy)

chromosome rearrangement :

Hin Recombinase (at The Online Macromolecular Museum). (Millard, Elizabeth; Downs, Aaron; Marcey, David)

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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))

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)

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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)

cloning :

Restriction Enzymes: Eco RV. (Reichsman, Frieda)

colicin :

Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)

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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)

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)

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complementarity-determining regions :

Antibody Recognition of Antigen (at The Online Macromolecular Museum). (Marcey, David)

complementarity-determining regions in antibody :

Antibody. (Martz, Eric)

concanavalin a :

Highlights of biochemistry: molecular structures made visible. (Bergmann, Rolf) (English or German)

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

Protein Structures List. (McClure, William)

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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 :

Morpher, Protein. (Martz, Eric)

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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

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

(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 :

Rubisco: a first look at the mechanism. An experiment in molecular visualisation. (Nixon, John)

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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)

Copper Blue :

The Guided Tours of Metalloproteins. (Morris, Robert; Lee, Adrian; Hadzovic, Alen)

copper proteins :

Redox Proteins. (Hansson, Orjan)

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