World Index of BioMolecular Visualization Resources

World Index of BioMolecular Visualization Resources Biochemical Structure Tutorials Titles Subjects Authors: Detailed Compact HOME Top 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 : The Glycolytic Cycle (Warren, L Van) 3-phosphoglycerate : The Glycolytic Cycle (Warren, L Van) Top 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 30S ribosomal subunit : Ribosome Tour (Decatur, Wayne) 30S ribosomal subunit : 70S Ribosome Architecture (McClure, Will) 3D Periodic Table of Radii: Cross-indexing terms: periodic table of the elements; elements, periodic table of; atomic radii; trends, periodic, in atomic and ionic sizes This image displays the elements as spheres arranged as in the periodic table The spheres have sizes proportional to the atomic, ionic and van der Waals radii The different neutral and ionic states are presented on different planes The site is designed to be viewed with Chime and there is also a set of buttons to create displays of only particular planes, elements, groups, periods, and coloring schemes The primary application is for a discussion of periodic trends in atomic and ionic size Author: Wherland, Scot Submitted by: the author (Entry 70) Submitted on Nov 1, 2000 3DEE : XdomView: A Chime-based Graphical Tool for Protein Domain and Exon Position Visualization (Gopalan, Vivek; Shoba Ranganathan; Tan Tin Wee) 434 repressor : Protein/DNA interactions (Gibson, Andrew; Sims, P F G.) Top 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 50S ribosomal subunit : Ribosome Tour (Decatur, Wayne) 50S ribosomal subunit : Large Ribosomal Subunit Tour (Decatur, Wayne) 50S ribosomal subunit : 70S Ribosome Architecture (McClure, Will) 70S Ribosome architecture : Ribosome Tour (Decatur, Wayne) 70S Ribosome architecture : 70S Ribosome Architecture (McClure, Will) A-DNA : Biomodel (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish) A-DNA : DNA Conformers (at The Online Macromolecular Museum) (Marcey, David) A-Form RNA helix : Structures for Molecular Biology (McClure, William) Top 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z α-Helix & β-Sheet in a Small Protein : Molecules for Modern/Cell Biology (McClure, William) α-lactalbumin (1b90.pdb), a human plasma transport protein : Protein Structures List (McClure, William) access to the active site : Rubisco: a first look at the mechanism An experiment in molecular visualisation (Nixon, John) Accessible, molecular and Van der Waals surfaces explained: Cross-indexing terms: surfaces; solvent accessible surface; molecular surface; van der Waals surface; YASARA An introduction to protein surfaces, explaining the difference between solvent accessible, molecular and Van der Waals surface Shows water molecules rolling across the protein Advanced tutorials about surface area calculations are available from the same page The tutorial requires (and comes with) YASARA View Author: Krieger, Elmar Submitted by: the author (Entry 152) Submitted on Aug 13, 2004 Top 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z acesulfame : Everything You Ever Wanted to Know about Sweeteners (Walters, D Eric) acetycholinesterase-edrophonium : Molecular Science Lab (Oberholser, Karl) Acetyl-CoA : Isoprenoid Biosynthesis Pathway (Warren, L Van) acetylcholinesterase inhibitors : Molecular Science Lab (Oberholser, Karl) Top 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 acetylcholinesterase mechanism : Molecular Science Lab (Oberholser, Karl) acetylcholinesterase- m-(N,N,N-trimethylammonio)trifluoroacetophenone : Molecular Science Lab (Oberholser, Karl) acetylcholinesterase-decamethonium : Molecular Science Lab (Oberholser, Karl) acetylcholinesterase-tacrine : Molecular Science Lab (Oberholser, Karl) Top 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z actinomycin : Highlights of biochemistry: molecular structures made visible (Bergmann, Rolf) (English or German) activators : Chime Square (Niederhoffer, Eric) active site : Carboxypeptidase A - Three Exercises with Chime (Morgan, Eleanor; Helmerhorst, Erik) Adenosine Kinase : The Lycoming College Macromolecular Modeling and Bioinformatics Page (Newman, Jeff) Top 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 Adenosine Triphosphate : Molecule of the Month/University of Bristol (May, Paul (editor)) ADP : The Glycolytic Cycle (Warren, L Van) Adrenaline : Molecule of the Month/University of Bristol (May, Paul (editor)) Advanced Protein Explorer : Protein Explorer, Advanced (Martz, Eric; (MSA3D component coauthored by Paul Stothard)) Top 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 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.) Top 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 albumin, serum : Garrett and Grisham Interactive Biochemistry Structure Tutorials (Caras, James) aldolase : The Glycolytic Cycle (Warren, L Van) alignment : Structural Alignment Program for Proteins (Gille, Christoph) Alkaline phosphatase: Cross-indexing terms: alkaline phosphatase; enzyme-substrate complex A lecture-oriented chime 'slide show' about alkaline phosphatase Buttons show particular views (these must usually be played in order) and a caption appears in the lowest frame This shows • the two subunits with active sites highlighted & substrate added • a close-up of the active site with critical substrate-enzyme bonds Author: White, Brian Submitted by: the author (Entry 79) Submitted on Nov 10, 2000 Alkaline phosphatase: Cross-indexing terms: alkaline phosphatase; enzyme-substrate complex A lecture-oriented chime 'slide show' about alkaline phosphatase Buttons show particular views (these must usually be played in order) and a caption appears in the lowest frame This shows • the two subunits with active sites highlighted & substrate added • a close-up of the active site with critical substrate-enzyme bonds Author: White, Brian Submitted by: the author (Entry 79) Submitted on Nov 10, 2000 Top 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z Alkohole, Kohlenhydrate, Carbonsaeuren, Aminosaeuren, Eiweisse : Chemie und Internet am Gymnasium (Rausch, Martin) (German) alpha helix : Protein Secondary Structure, versions 1.0, 2.0, 3.0 (Reichsman, Frieda; Driscoll, Tim) alpha helix : Introduction to Protein Structure (Gorga, Frank) alpha-helix : Introduction to Protein Structure, Part I (Bragin, Victoria (Vicki)) alpha-helix : Biomodel (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish) alpha-helix : Animations on subjects of Structural and Metabolic Biochemistry (Silva, Pedro) Alzheimer's : Highlights of biochemistry: molecular structures made visible (Bergmann, Rolf) (English or German) Top 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z amino acid : Molecules and Structures Homepage (Gasser, Charles) amino acid chemistry : Introduction to Protein Structure (Gorga, Frank) Amino Acid Identification Quiz: Cross-indexing terms: lesson plan; quiz; amino acids Quiz in a frames format; the user is required to identify the 20 amino acids shown as Chime images by name, abbreviation, and/or one-letter code Answers are provided after each selection, and a running total of correct and incorrect responses is tabulated Author: McClure, William Submitted by: the author (Entry 28) Submitted on Jun 1, 2000 Amino Acid Quizzer: Cross-indexing terms: quizzer, amino acid; lesson plan, amino acid quizzer At 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, sidechain 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) Top 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z Amino Acid Structure Quiz: Cross-indexing terms: quiz, amino acid structure; lesson plan Fifteen questions that cover all 20 amino acids, answered by clicking on the correct atoms in static snapshots of spacefilling or ball-and-stick models Hints are available Author: McClure, William Submitted by: Martz, Eric (Entry 149) Submitted on May 16, 2004 Amino Acid Structures : Online Macromolecular Museum (Marcey, David; Students at California Lutheran University; Students at Kenyon College) amino acids : Protein Architecture at Biochemistry in 3D (Driscoll, Timothy; Reichsman, Frieda) amino acids : Amino Acid Identification Quiz (McClure, William) amino acids : Course Home Page for "Computer Applications in Biotechnology" (Klevickis, Cindy) amino acids : Sickle Cell Anemia: Understanding the Molecular Biology (Sabo, John; Lynch, Jamie; Raineri, Deanna) amino acids : Biomodel (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish) amino acids : Biomolecular Structures (Hansson, Orjan) Amino Acids & Peptides : Molecules for Modern/Cell Biology (McClure, William) Top 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z amino acids and properties : The 20 common amino acids (Bragin, Victoria (Vicki); Johnston, Wendie) amino acids, all 20 : Side-by-Side Amino Acid Viewer (McClure, William) aminoacyl-tRNA synthetase : Biomodel (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish) Anatoxin : Molecule of the Month/University of Bristol (May, Paul (editor)) Top 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z animated gifs : Course Home Page for "Computer Applications in Biotechnology" (Klevickis, Cindy) animation of translation in the ribosome : 70S Ribosome Architecture (McClure, Will) animation with XYZ files : Thermal motion of alpha helix (Cachau, Raul E.) animations : Lac repressor bending DNA operon (Martz, Eric) Top 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z animations of vibrations, infrared spectra : Infrared spectra, animations of vibrational modes (Motyka, Eric; Lahti, Paul; Lancashire, Robert J.) Animations on subjects of Structural and Metabolic Biochemistry: Cross-indexing terms: alpha-helix; beta-sheet; oxyhemoglobin; deoxyhemoglobin; cytochrome c oxidase; succinate dehydrogenase; cytochrome bc1; respiratory chain complexers; electron transport chain Chime-based tutorials on protein secondary, structure, hemoglobin and electron-transfer complexes More will eventually follow Author: Silva, Pedro Submitted by: the author (Entry 148) Submitted on Mar 15, 2004 Last revised on Mar 15, 2004 antibiotics : Highlights of biochemistry: molecular structures made visible (Bergmann, Rolf) (English or German) antibodies : AHo's Amazing Atlas of Antibody Structure (Honegger, Annemarie) Top 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z Antibody: Cross-indexing terms: immunoglobulin and Ig domains; IgG; epitope structure, lysozyme bound to antibody; disulfide bonds in immunoglobulin; complementaritydetermining regions in antibody; glycosylation of antibody, N-linked; lesson plan, antibody 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 CDR's identified, paratope contact atoms vs CDR's, epitope contact atoms, the flat and discontinuous character of the epitope, F(ab')2 and interchain disulfide bonds, intact IgG1, and the location and attachment of carbohydrate Buttons can be pushed in any order yet always give the same images Font size can be dymanically changed for large audiences The utilities menu enables recentering, atom identification, measuring distances, and changing background color from black to white for printing A list of questions is provided which can be printed and handed out to a class as a focus worksheet (lesson plan) Downloadable for off-line use, local installation or modification Author: Martz, Eric Submitted by: the author (Entry 14) Submitted on May 28, 2000 Last revised on Oct 3, 2004 Antibody : AHo's Amazing Atlas of Antibody Structure (Honegger, Annemarie) Antibody : BioMolecular Explorer 3D: Resources for High School Biology (Reichsman, Frieda; Eric Martz) Antibody Recognition of Antigen : Online Macromolecular Museum (Marcey, David; Students at California Lutheran University; Students at Kenyon College) Antibody Recognition of Antigen (at The Online Macromolecular Museum): Cross-indexing terms: hypervariable regions, immunoglobulin; immunoglogulin binding; complementarity-determining regions; CDRs This exhibit uses three examples of antibody-antigen complexes to illustrate some structural features of antibody recognition of epitope Antibody bound to a globular protein antigen is followed by an examination of the mechanisms of peptide antigen binding The exhibit finishes with a look at antibody recognition of a small antigenic molecule, a hapten Author: Marcey, David Submitted by: the author (Entry 115) Submitted on Jun 18, 2001 antibody structure : Immunoglobulin Structure (at The Online Macromolecular Museum) (Marcey, David) Top 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z antiparallel strands : DNA Structure (at The Online Macromolecular Museum) (Marcey, David) apoptosis, programmed cell death, caspases, NF-kappa B, Ik-B, bcl-2, IAP : Molecular Visualizations on Apoptosis (Pons, Gabriel; Gil, Joan) (Spanish) AQP1 Aquaporin Channel (1j4n.pdb) : Membrane Channel & Pump Structures (McClure, William) archaeal rhodopsins : Highlights of biochemistry: molecular structures made visible (Bergmann, Rolf) (English or German) Top 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z aromatic sidechains: face-to-face, side-to-face, face-to-cation : Noncovalent Interactions in Proteins (Cox, Ricky) ASBMB : 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) Top 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z atomic radii : 3D Periodic Table of Radii (Wherland, Scot) ATP : Molecule of the Month/University of Bristol (May, Paul (editor)) ATP : Molecules for Modern/Cell Biology (McClure, William) ATP : The Glycolytic Cycle (Warren, L Van) authoring new Chime websites, methods : How to Create New Chime Tutorials (Martz, Eric) azt : HIV-1 Reverse Transcriptase (at The Online Macromolecular Museum) (Goldman, Matthew; Marcey, David) Top 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z B-DNA : Biomodel (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish) B-DNA : DNA Conformers (at The Online Macromolecular Museum) (Marcey, David) B-DNA : DNA Structure (at The Online Macromolecular Museum) (Marcey, David) B-Form Deoxyribonucleic Acid (DNA): Cross-indexing terms: deoxyribonucleic acid, DNA, major groove, minor groove This Chime resource contains animations to illustrate the structure of DNA The animations are initiated by clicking buttons on the right pannel They show a base pair in the context of a larger helix and highlight the bases, sugars and phosphates You can see how the helix is created by observing the structure of a two and three base pair helix The last animation emphasizes how the major and minor grooves are created The DNA coordinates were generated by Sybyl using idealized coordinates for B-DNA Author: Bruist, Michael Submitted by: the author (Entry 85) Submitted on Jan 19, 2001 B-Form DNA helix : Structures for Molecular Biology (McClure, William) bacterial photosynthesis : Highlights of biochemistry: molecular structures made visible (Bergmann, Rolf) (English or German) Top 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z bacteriophage cro : Cro Repressor of Temperate Bacteriophages (at The Online Macromolecular Museum) (Marcey, David) bacteriophage repressor : Cro Repressor of Temperate Bacteriophages (at The Online Macromolecular Museum) (Marcey, David) Bacteriorhodopsin: Cross-indexing terms: bacteriorhodopsin (1brx.pdb) A one-page Chime display of nine recent bacteriorhodopsin structures and links to the PubMed entries for the structure references Author: McClure, William Submitted by: the author (Entry 24) Submitted on Jun 1, 2000 bacteriorhodopsin (1brx.pdb) : Bacteriorhodopsin (McClure, William) Top 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z Bacteriorhodopsin (1c3w.pdb, 1dze.pdb) : Membrane Channel & Pump Structures (McClure, William) Bacteriorhodopsin (Br.pdb), a light-driven proton pump : Protein Structures List (McClure, William) Bacteriorhodopsin: A membrane-spanning protein : Molecules for Modern/Cell Biology (McClure, William) BamHI endonuclease : Online Macromolecular Museum (Marcey, David; Students at California Lutheran University; Students at Kenyon College) Top 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z BamHI Restriction Endonuclease (at The Online Macromolecular Museum): Cross-indexing terms: Type II restriction endonuclease; restriction enzymes; DNAbinding 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 Chimebased exhibit focuses on the structure-function relationships of BamHI Authors: Silva, Nathan; Leslie, Kenneth; Marcey, David Submitted by: Marcey, David (Entry 100) Submitted on Jun 17, 2001 base pairing : Sickle Cell Anemia: Understanding the Molecular Biology (Sabo, John; Lynch, Jamie; Raineri, Deanna) base pairs : DNA Structure (Reichsman, Frieda) (English, Italian) basic biochemistry for undergrads : Biomolecular Structures (Hansson, Orjan) Top 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z Bence-Jones protein REI monomer & dimer : Molecular Science Lab (Oberholser, Karl) bending of DNA : Lac repressor bending DNA operon (Martz, Eric) beta barrel : GFP (Green Fluorescent Protein) (Driscoll, Timothy) beta pleats : Introduction to Protein Structure, Part I (Bragin, Victoria (Vicki)) Top 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z beta sheet : Protein Secondary Structure, versions 1.0, 2.0, 3.0 (Reichsman, Frieda; Driscoll, Tim) beta sheet : Introduction to Protein Structure (Gorga, Frank) beta-elimination : Rubisco: a first look at the mechanism An experiment in molecular visualisation (Nixon, John) beta-sheet : Biomodel (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish) beta-sheet : Animations on subjects of Structural and Metabolic Biochemistry (Silva, Pedro) bilayer, lipid : Biomodel (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish) bilayer, lipid : Lipid Bilayers and the Gramicidin Channel (Martz, Eric; Herraez, Angel) Top 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z BioEditor : Zinc Binuclear Clusters (Craig, Paul) Biomodel: (Spanish ) Cross-indexing terms: amino acids; peptides; proteins; alpha-helix; beta-sheet; collagen; hemoglobin; immunoglobulin; DNA; A-DNA; B-DNA; Z-DNA; RNA; rRNA; tRNA; nucleosome; helix-turn-helix; helix-loop-helix; homeodomain; leucine zipper; zinc finger; aminoacyl-tRNA synthetase; bilayer, lipid; lipid bilayer; gramicidin channel; rybozymes; Rev protein; RBE; EF-Tu; U1A; spliceosome Self-guided tutorial, emphasizing 3D-structure and interaction between macromolecules It is in Spanish Runs as Chime models inside an explanatory web page Allows both guided tour and user-chosen pathway and action on models Biomodel-1 covers amino acids, peptides, secondary, tertiary and quaternary structure of proteins (exemplified by alpha-helix, beta-sheets, collagen, hemoglobin and immunoglobulins), DNA (A-, B- and Z- forms), RNA, and interactions of nucleic acids with protein motifs (nucleosome, helix-turn-helix, helix-loop-helix, homeodomain, leucine zipper, zinc finger, and RNA-protein complexes) Addressed to University students of Biochemistry and Molecular Biology Biomodel-2: a Chime version of Eric Martz's Rasmol script on bilayer membranes and gramicidin channel Biomodel-3 is a lower-level module addressed to secondary school students, includes sugars, lipids, some vitamins, amino acids, proteins, bases, nucleosides, nucleotides and nucleic acids Authors: Herraez, Angel; Lopez-Lopez, Jose Ramon Submitted by: the author (Entry 89) Submitted on Mar 13, 2001 Last revised on Jul 8, 2002 BioMolecular Explorer 3D: Resources for High School Biology: Cross-indexing terms: antibody; collagen; DNA; hemoglobin; HIV; protease; protease inhibitor; HIV-protease inhibitor; AIDS; lactase; lac repressor; lipid bilayers; myosin; nucleosome; water; high school; high school biology; lesson plan; Chime BioMolecular Explorer 3D is a website designed to provide high school teachers with interactive 3D structures of biologically significant molecules that fit in high school biology curricula The following resources are available at BioMolecular Explorer 3D: Links to software for viewing and exploring molecules in 3D o download the software o follow our instructions for installing it Pre-selected biomolecules that fit well in a high school biology curriculum o each molecule is placed in its biological context with a brief description o each molecule is linked to an interactive 3D display (assuming prior installation of software) Assistance with lesson planning o each molecule is linked to background information specially selected for HS teachers Access to additional molecules o we show you where to find many other biomolecular 3D displays and tutorials Authors: Reichsman, Frieda; Eric Martz Submitted by: the author (Entry 160) Submitted on Dec 14, 2004 Biomolecular Structures: Cross-indexing terms: amino acids; peptides; basic biochemistry for undergrads; protein structure; nucleotides; DNA; RNA; lesson plan Biomolecular Structures is an Internet tutorial intended as a computer-based laboratory exercise for undergraduate students in basic biochemistry It covers the basic properties of amino acids, peptides, proteins, nucleotides and nucleic acids The tutorial makes use of the Chemscape Chime plug-in and JavaScript Particular attention has been paid to the design of the user interface so that students which are not so experienced with computers can navigate easily through the course A form with simple questions is included Extensive help is available to guide the user Author: Hansson, Orjan Submitted by: the author (Entry 132) Submitted on Jun 7, 2002 Last revised on Jun 7, 2002 Top 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 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 Sickle Cell Anemia: Understanding the Molecular Biology: Cross-indexing terms: mRNA; introns; exons; DNA; base pairing; amino acids; transcription; translation; mutations; stop codons; reading frames; hemoglobin; disease This tutorial was created in order to demonstrate how a single nucleotide substitution in one of the beta-globin chains of human hemoglobin leads to the disease, sickle cell anemia The Biology Workbench is used to align a "normal" or "wildtype" beta-globin sequence with a mutated or sickle cell sequence to show the location of the mutation The Protein Explorer program is then used to identify the affected amino acid in the beta-globin protein chain and to visualize how the mutation changes the structure and conformation of the hemoglobin molecule Chime version 2.0.3 is needed on PCs and version 2.0a for Macs Authors: Sabo, John; Lynch, Jamie; Raineri, Deanna Submitted by: Raineri, Deanna (Entry 75) Submitted on Nov 9, 2000 Last revised on Mar 25, 2001 sickle hemoglobin : Hemoglobin (Martz, Eric) Top 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 sickle-cell anemia : Hemoglobin II (White, Brian) Side-by-Side Amino Acid Viewer: Cross-indexing terms: amino acids, all 20; Met-enkephalin; oxytocin; peptides and peptide bond In a frames format, the selection forms above each frame let you view each of the 20 amino acids using the Chemscape Chime Plug-in The buttons in each frame highlight side chain functional groups, overall dimensions, and side chain polarity The last six entries in the selection lists are peptides In addition to highlighting features of the peptide bond, these models serve as a review of amino acid side-chain structures Author: McClure, William Submitted by: the author (Entry 20) Submitted on Jun 1, 2000 side-chain interactions : Hemoglobin I (White, Brian) sidechain : Introduction to Protein Structure, Part I (Bragin, Victoria (Vicki)) Top 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 signal recognition : Signal Recognition Particle Core (at The Online Macromolecular Museum) (Marcey, David) Signal Recognition Particle: Cross-indexing terms: SRP, the E coli signal recognition particle, (1dul.pdb); E coli Ffh protein: the protein subunit without RNA (2ffh.pdb); Domain IV RNA Structure (1cq5.pdb) A one-page Chime display of the signal recognition particle (SRP) shows the M domain of E coli Ffh protein complexed with domain IV of 4.5S RNA (1dul.pdb) There are also links to similar Chime displays of: Domain IV RNA Structure: the average NMR structure of the RNA alone (1cq5.pdb) Ffh protein: the protein subunit without RNA (2ffh.pdb) All three models in a side-by-side display on one page Author: McClure, William Submitted by: the author (Entry 23) Submitted on Jun 1, 2000 Last revised on Jun 3, 2000 Signal Recognition Particle Core (at The Online Macromolecular Museum): Cross-indexing terms: signal recognition; protein targeting; SRP In both eukaryotes and prokaryotes, a signal recognition particle (SRP) is responsible for recognizing and binding to a signal sequence at the amino terminus of a growing, membrane-bound protein This is essential for targeting the protein to the membrane This exhibit focuses on the structure of the SRP core of E coli, which represents an evolutionarily preserved core of the SRP in all organisms Author: Marcey, David Submitted by: the author (Entry 114) Submitted on Jun 18, 2001 Signal Recognition Particle Core (E coli) : Online Macromolecular Museum (Marcey, David; Students at California Lutheran University; Students at Kenyon College) Top 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 sildenafil : Highlights of biochemistry: molecular structures made visible (Bergmann, Rolf) (English or German) sildenafil : The Rational Basis of Drug Design (Walters, D Eric) Silk Protein (2slk.pdb), a theoretical model of the fibrous β-sheet protein : Protein Structures List (McClure, William) simulation, theoretical, water : Water Simulation (Martz, Eric) Singapore : XdomView: A Chime-based Graphical Tool for Protein Domain and Exon Position Visualization (Gopalan, Vivek; Shoba Ranganathan; Tan Tin Wee) Top 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 Sliding DNA clamp : DNA Polymerase III-Beta Subunit (at The Online Macromolecular Museum) (Marcey, David) slowest enzyme : Rubisco: a first look at the mechanism An experiment in molecular visualisation (Nixon, John) Small Molecule Lab Exercise: Cross-indexing terms: amino acid quizzer; lab exercise In the first page, students are given a few simple structures to draw from the chime image This familiarizes them with the interface & the representation used by chime In the second page, they randomly select amino acids by number from a protein and must identify them by structure Author: White, Brian Submitted by: the author (Entry 80) Submitted on Nov 10, 2000 small molecules : Molecular Visualization Resources for Project VISM (Klevickis, Cindy) Top 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 SN1 reaction : DNA Polymerase I from Thermus aquaticus (Bruist, Michael) snRNP : U1A Spliceosomal Protein (at The Online Macromolecular Museum) (Marcey, David) snRNP U1A : Structures for Molecular Biology (McClure, William) solvent accessible surface : Accessible, molecular and Van der Waals surfaces explained (Krieger, Elmar) Top 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 SOS response : RecA Protein (at The Online Macromolecular Museum) (Heerssen, Heather; Downs, Aaron; Marcey, David) SP1 : Molecules and Structures Homepage (Gasser, Charles) spermine : Course Home Page for "Computer Applications in Biotechnology" (Klevickis, Cindy) Spliceosomal Protein-RNA Interactions, U1A : Online Macromolecular Museum (Marcey, David; Students at California Lutheran University; Students at Kenyon College) Top 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 spliceosome : Biomodel (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish) Splicesomal Protein : U1A Spliceosomal Protein (at The Online Macromolecular Museum) (Marcey, David) Squalene : Isoprenoid Biosynthesis Pathway (Warren, L Van) src-family : Explore the c-Src tyrosine kinase (Engen, John R; Superti-Furga, Giulio) Top 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 SRP : Signal Recognition Particle Core (at The Online Macromolecular Museum) (Marcey, David) SRP, the E coli signal recognition particle, (1dul.pdb) : Signal Recognition Particle (McClure, William) Staurosporine : Molecule of the Month/University of Bristol (May, Paul (editor)) stem-loop : Hammerhead Ribozyme (Reichsman, Frieda) Top 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 stereoelectronic control : Rubisco: a first look at the mechanism An experiment in molecular visualisation (Nixon, John) stereoisomerism : Web-Based Chemical Investigations (Bragin, Victoria (Vicki)) Steroids : Isoprenoid Biosynthesis Pathway (Warren, L Van) stop codons : Sickle Cell Anemia: Understanding the Molecular Biology (Sabo, John; Lynch, Jamie; Raineri, Deanna) Top 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 Structural Alignment Program for Proteins: Cross-indexing terms: alignment; protein superposition; pymol; jmol; rasmol; vmd; mutations; residue annotation; java; multiple structure alignment STRAP is an interactive editor for multiple sequence alignments of proteins Several tutorials and wizards on the following topics are integrated in STRAP: mapping of mutations and polymorphisms onto three-dimensional protein structures multiple structure alignments BLAST searches evolutionary dendrograms multiple sequence alignments of sequences with little similarity These tutorials are the basis for training courses which are offered for students of biophysics, biochemistry and biology at the Humboldt University Berlin Author: Gille, Christoph Submitted by: the author (Entry 158) Submitted on Oct 27, 2004 Structural Biochemistry of Blood Coagulation: Cross-indexing terms: blood coagulation; tissue factor; factor II; factor III; factor VII; factor IX; factor XIII; von Willebrand factor; protein C; thrombin; hirudin; fibrin The structures of many blood coagulation factors have been determined experimentally by Xray crystallography or by NMR spectroscopy These pages illustrate structural features of these proteins using Chime Included are tissue factor (factor III); a tissue factor + factor VII complex; von Willebrand factor; tissue factor pathway inhibitor; protein C; a portion of factor IX containing several gamma-carboxy-glutamate residues; thrombin (factor II, complexed with hirudin, a leech anticoagulant); factor XIII; a fibrin fragment Author: Walters, D Eric Submitted by: the author (Entry 73) Submitted on Nov 6, 2000 structural domain : XdomView: A Chime-based Graphical Tool for Protein Domain and Exon Position Visualization (Gopalan, Vivek; Shoba Ranganathan; Tan Tin Wee) structure and mechanism : Rubisco: a first look at the mechanism An experiment in molecular visualisation (Nixon, John) Top 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 structure, protein, primary, secondary : Introduction to Protein Structure, Part I (Bragin, Victoria (Vicki)) structure-activity relationships : The Rational Basis of Drug Design (Walters, D Eric) Structures for Molecular Biology: Cross-indexing terms: B-Form DNA helix; A-Form RNA helix; cAMP Receptor Protein (CRP); Yeast GAL4 Protein; Human hnRNP A1; snRNP U1A; EF-Tu, tRNAPhe, and GTP; Zif268 zinc finger; EcoRI Res Endonuclease; HhaI Res Methylase; Nucleosome An index table of structures for molecular biology courses PubMed entries and Chime displays of the structures can be viewed by following the links provided Author: McClure, William Submitted by: the author (Entry 27) Submitted on Jun 1, 2000 strucuture : XdomView: A Chime-based Graphical Tool for Protein Domain and Exon Position Visualization (Gopalan, Vivek; Shoba Ranganathan; Tan Tin Wee) Top 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 Student Webpapers: The Structure-Function Relationships for the Enzymes in the Glycolytic and Lactate Fermentation Pathways.: Cross-indexing terms: glycolysis; gluconeogenesis; lactate fermentation; Classroom use of Chime; lesson plan Students taking Chem406 at the University of Wisconsin-Eau Claire are required to write a Web termpaper (Webpaper) that reviews the structure-function relationships of a protein Chem406 is a biophysical chemistry course that is required of undergraduate students majoring in Biochemistry/Molecular Biology For the Fall 1999 semester the students were assigned enzymes from the glycolytic, gluconeogenesis, and lactate fermentation pathways The students were required to use Chime images to illustrate their papers and to use JavaScript buttons to modify these images in context with the narrative of their paper We have found Web page authoring with Chimes to be a powerful tool for teaching students about the structure/function relationships of proteins The homepage for this site contains two links: one to the detailed assignment that was given to the students, the other to a figure showing the metabolic pathways involved Each enzyme named in this figure provides a link to a student Webpaper These are student-authored reports, unedited by faculty, consequently the quality and accuracy does vary All together there are 12 Webpapers with a average of three Chimes per Webpaper The specific enzymes covered include: • Hexokinase (E.C.2.7.1.1) • Glucose 6-Phosphate Isomerase (E.C.5.3.1.9) • Phosphofructokinase (E.C.2.7.1.11) • Fructose 1,6-Bisphosphate Aldolase (E.C 4.1.2.13) • Triosephosphate Isomerase (E.C 5.3.1.1) • Glyceraldehyde 3-Phosphate Dehydrogenase (E.C 1.2.1.12) • 3-Phosphoglycerate Kinase (E.C 2.7.2.3) • 3-Phosphoglycerate Mutase (E.C 5.4.2.1) • 2-Phosphoglycerate Hydrolase (Enolase) (E.C 4.2.1.11) • Pyruvate Kinase (E.C 2.7.1.40) • Fructose 1,6-Bisphosphatase (E.C 3.1.3.11) • Lactate Dehydrogenase (E.C 1.1.1.27) Author: Chem406 Class, Fall 1999, U Wisc-Eau Claire Submitted by: Gallagher, Warren (Entry 57) Submitted on Aug 10, 2000 student-authored tutorials : Course Home Page for "Computer Applications in Biotechnology" (Klevickis, Cindy) substrate binding : Magnesium Adenosine Triphosphate (MgATP) Binding to an Enzyme (Bruist, Michael) succinate dehydrogenase : Animations on subjects of Structural and Metabolic Biochemistry (Silva, Pedro) Top 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 sucralose : Everything You Ever Wanted to Know about Sweeteners (Walters, D Eric) Sucrose -> Fructose & Glucose : Molecules for Modern/Cell Biology (McClure, William) Sulfanilamide : Molecule of the Month/University of Bristol (May, Paul (editor)) supersecondary motifs : Protein Architecture at Biochemistry in 3D (Driscoll, Timothy; Reichsman, Frieda) Top 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 surfaces : MolUSc - Molecules pour un Usage Scholaire (Pillot, Paul) (French) surfaces : Accessible, molecular and Van der Waals surfaces explained (Krieger, Elmar) SV40 capsid structure and assembly.: Cross-indexing terms: Presentation in Protein Explorer (PIPE - prototype); VP1; virus capsid structure; icosahedral capsid structure The major component of the Simian Virus 40 capsid is 360 copies of VP1 This is a detailed tour of how VP1 fits into pentamers, and how the 72 pentamers assemble to form an icosahedral capsid It ends with a rotatable 'soccer ball' image of the capsid within an icosahedron In addition to 30 views in Chime, schematic diagrams are included, and this presentation is a prototype within Protein Explorer 1.0 This means you can use the full capabilities of Protein Explorer to manipulate any view in the presentation (An earlier version of this SV40 tutorial is available at Univ Massachusetts.) Author: Welte, Stefan Submitted by: the author (Entry 7) Submitted on May 25, 2000 Last revised on Dec 16, 2000 sweetener : Everything You Ever Wanted to Know about Sweeteners (Walters, D Eric) SYBYL : Macromolecular Visualization Laboratory Exercise (Kahn, Kalju) Top 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 Tamoxifen : Molecule of the Month/University of Bristol (May, Paul (editor)) TATA box binding protein : Highlights of biochemistry: molecular structures made visible (Bergmann, Rolf) (English or German) TATA-binding protein : Molecules and Structures Homepage (Gasser, Charles) Tc3 transposase : Biomolecules at Kenyon College (Students, Kenyon College; Site Director, Joan Slonczewski) (English; CopG auf Deutch) Top 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 template : DNA Polymerase I from Thermus aquaticus (Bruist, Michael) tertiary structure : Protein Architecture at Biochemistry in 3D (Driscoll, Timothy; Reichsman, Frieda) tertiary structure : Introduction to Protein Structure, Part I (Bragin, Victoria (Vicki)) tertiary structure : Introduction to Protein Structure (Gorga, Frank) Tetrodotoxin : Molecule of the Month/University of Bristol (May, Paul (editor)) TFIIIA : Molecules and Structures Homepage (Gasser, Charles) Top 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 Thalidomide : Molecule of the Month/University of Bristol (May, Paul (editor)) The 20 common amino acids: Cross-indexing terms: amino acids and properties; lesson plan Each amino acid is displayed (with hydrogens) in Chime in a table including names, structural formulae, pI and pK values A list of questions for a class is provided as a lesson plan (click the separate link "Exploring Amino Acids and Proteins - An Internet Assignment for Biology Students") Most of the questions can be answered from the table of amino acids, but some extend to electrophoresis, and the uses of other websites to determine isoelectric points of arbitrary peptides, and the use of Entrez to find protein sequences Authors: Bragin, Victoria (Vicki); Johnston, Wendie Submitted by: the author (Entry 63) Submitted on Aug 17, 2000 Last revised on Mar 19, 2001 The E coli trp Repressor Chime Movie: Cross-indexing terms: trp repressor; trpR; repressor; trp operator; operator; DNA binding protein; ligand activation; tryptophan This Chime movie illustrates the structural differences between crystal structures of the inactive apo form (3WRP) and liganded active form (1TRO) of trp repressor, a DNA binding protein from E coli Both structures are superimposed in a single PDB file which is downloaded to the left frame Apo vs holo forms are selected by toggling push buttons, and the trp operator DNA can also be toggled on and off The site was designed to make it possible to easily compare these structures, and to illustrate one of few examples where the structural basis for ligandactivation of a DNA-binding protein has been clearly elucidated using crystal structure analysis Author: Lawson, Cathy Submitted by: the author (Entry 68) Submitted on Sep 24, 2000 The Glycolytic Cycle: Cross-indexing terms: glucose; hexokinase; ATP; ADP; phosphoglucoisomerase; phosphofructokinase; aldolase; glyceraldehyde-3-phosphate; phosphoglycerate kinase; 3-phosphoglycerate; phosphoglycerate mutase; 2-phosphoglycerate; enolase; 2-phosphoenolpyruvate; pyruvate kinase; pyruvate; lactate dehydrogenase; lactate Chime is used to illustrate each step in the glycolytic cycle including the full structure of each substrate and enzyme and the free energy change occurring at each step Author: Warren, L Van Submitted by: the author (Entry 60) Submitted on Aug 15, 2000 Top 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 The Large Ribosomal Subunit: a structure/function tutorial: Cross-indexing terms: protein synthesis; enzyme mechanism; translation; rRNA; tRNA; ribosome By this point, the ribosome should be a familiar object in your biochemistry/biology education because all life as we know it requires a ribosome to construct proteins The peptide bond formation it catalyzes is rather simple; however, the complete molecule must also read mRNA codons, and bind tRNA molecules This accounts, in part, for the large size of the molecule Unfortunately, much of the mechanism remains a mystery In a series of papers published in 2000, researchers have determined the structure of the large subunit to a great degree of accuracy, and have proposed specific residues which catalyze the peptide bond formation in large subunit In this tutorial, we will examine the large subunit, and in doing so, will address three related questions Which of the components of the large subunit comprise the active site, where is that site located, and how does it work? This tutorial uses the Chime plugin to visualize the three dimensional structure of the ribosome and to animate the mechanism of peptide formation Authors: Sontum, Stephen; Lesko, Zack Submitted by: the author (Entry 147) Submitted on Feb 12, 2004 The Lycoming College Macromolecular Modeling and Bioinformatics Page: Cross-indexing terms: HIV protease; Ribosomal small subunit; Adenosine Kinase; Dystrophin; G-protein Beta and Gamma subunits; DNA glycosylase; Clathrin; Fibronectin; Myosin; Insulin receptor; Dihydrofolate reductase The Bioinformatics exercises at Lycoming were designed to use Biowire.com's Jellyfish software 3-D protein structure tutorials require the Chime plug-in The students have produced Integrated Informatics Projects (99-04) and Protein Structure/Function Projects (98-99) that illustrate the structures and functions of many proteins Author: Newman, Jeff Submitted by: Foley, Brian (Entry 159) Submitted on Nov 1, 2004 The Rational Basis of Drug Design: Cross-indexing terms: drug discovery; HIV; inhibitor, protease; protease inhibitor; HIV-protease inhibitor; saquinavir; indinavir; ritonavir; sildenafil; Viagra; structure-activity relationships Supplementary materials for a series of graduate lectures on the discovery of new drugs Includes numerous chemical structures and several Chime structures Illustrated with detailed descriptions of the development of HIV protease inhibitors and the discovery of sildenafil (Viagra) Author: Walters, D Eric Submitted by: the author (Entry 74) Submitted on Nov 6, 2000 The Zinc Finger: A Protein Domain that Binds Specific DNA Sequences: Cross-indexing terms: DNA binding protein; zinc finger; zif268; protein secondary structure; lesson plans A zinc finger-DNA complex is used to introduce protein structure Initially, a single finger (without DNA) is viewed It consists of a beta hairpin and an alpha helix Various parts of this structure can be viewed separately The students are asked a few simple questions regarding the structure Answers are available with a click Then, a three-figer structure and the DNA it binds is viewed Again different parts of the complex can be selected A few questions are asked of the structure Answers are provided Author: Bruist, Michael Submitted by: the author (Entry 137) Submitted on Sep 10, 2002 Top 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 theoretical simulation of water : Water Simulation (Martz, Eric) Thermal motion of alpha helix: Cross-indexing terms: XYZ format animation; animation with XYZ files Molecular dynamics simulation of thermal motion of a 12-residue polyalanine right-handed helix unfolding This illustrates Chime's ability to display animations using XYZ-format atomic coordinate files Note that unlike PDB files, XYZ files lack information about residue names or atom positions within residues (e.g alpha carbon) Hence for proteins, NMR-format PDB files are preferable (see the Morpher) Author: Cachau, Raul E Submitted by: Martz, Eric (Entry 53) Submitted on Aug 8, 2000 thermophilic red alga : Rubisco: a first look at the mechanism An experiment in molecular visualisation (Nixon, John) thiolate ligand : Cytochrome P450 3D structures page (Nelson, David) Top 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 thrombin : Structural Biochemistry of Blood Coagulation (Walters, D Eric) timing of active site closure : Rubisco: a first look at the mechanism An experiment in molecular visualisation (Nixon, John) tissue factor : Structural Biochemistry of Blood Coagulation (Walters, D Eric) tobacco mosaic virus : Highlights of biochemistry: molecular structures made visible (Bergmann, Rolf) (English or German) Top 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 Topoisomerase I : Online Macromolecular Museum (Marcey, David; Students at California Lutheran University; Students at Kenyon College) topoisomerase, type I : DNA Topoisomerase I (at The Online Macromolecular Museum) (Kysela, David; Marcey, David) toxoplasmosis : Highlights of biochemistry: molecular structures made visible (Bergmann, Rolf) (English or German) transcription : Sickle Cell Anemia: Understanding the Molecular Biology (Sabo, John; Lynch, Jamie; Raineri, Deanna) transcription : Lac Repressor: Biochemistry in 3D (Driscoll, Timothy) Top 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 transcription activation : Estrogen Receptor Structures & Function (McClure, Will; Saha, Suparna) transcription activator : Zinc Binuclear Clusters (Craig, Paul) transcription factor : Nitrogen Regulatory Protein C (at The Online Macromolecular Museum) (Carroll, Carla; Marcey, David) transcription factor : Molecules and Structures Homepage (Gasser, Charles) transcription factors : Chime Square (Niederhoffer, Eric) Top 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 transcription regulation : Cro Repressor of Temperate Bacteriophages (at The Online Macromolecular Museum) (Marcey, David) transcriptional regulation : Lac Repressor: Biochemistry in 3D (Driscoll, Timothy) transfer RNA : Macromolecular Visualization Laboratory Exercise (Kahn, Kalju) translation : Sickle Cell Anemia: Understanding the Molecular Biology (Sabo, John; Lynch, Jamie; Raineri, Deanna) translation : Large Ribosomal Subunit Tour for Specialists (Decatur, Wayne) translation : Ribosome Tour (Decatur, Wayne) translation : Large Ribosomal Subunit Tour (Decatur, Wayne) translation : The Large Ribosomal Subunit: a structure/function tutorial (Sontum, Stephen; Lesko, Zack) Top 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 translation (animation) and ribosome structure : 70S Ribosome Architecture (McClure, Will) transport : Highlights of biochemistry: molecular structures made visible (Bergmann, Rolf) (English or German) trends, periodic, in atomic and ionic sizes : 3D Periodic Table of Radii (Wherland, Scot) Tricarboxylic acid cycle : Images of TCA Cycle Intermediates (McClure, William) Top 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 Triose Phosphate Isomerase (1ypi.pdb), a parallel β-barrel with alternating βαβ motifs : Protein Structures List (McClure, William) tRNA : Nucleic Acid Structure Tutorials (Nolan, Jim) tRNA : Biomodel (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish) tRNA : Ribosome Tour (Decatur, Wayne) tRNA : The Large Ribosomal Subunit: a structure/function tutorial (Sontum, Stephen; Lesko, Zack) tRNA synthetase : Biomolecules at Kenyon College (Students, Kenyon College; Site Director, Joan Slonczewski) (English; CopG auf Deutch) tRNA synthetase : Macromolecular Visualization Laboratory Exercise (Kahn, Kalju) tRNA Tour: Cross-indexing terms: tRNAPhe (6tna.pdb) In a frames format, this Chime-based tutorial displays the secondary and tertiary structural features of yeast tRNAPhe It is designed to complement the description in Saenger, W (1984) Principles of Nucleic Acid Structure Ch 15 "tRNA-A Treasury of Stereochemical Information" Author: McClure, William Submitted by: the author (Entry 31) Submitted on Jun 1, 2000 Top 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 tRNAPhe (6tna.pdb) : tRNA Tour (McClure, William) Tropomyosin (2tma.pdb), a fibrous coiled-coil protein : Protein Structures List (McClure, William) trp operator : The E coli trp Repressor Chime Movie (Lawson, Cathy) trp repressor : Protein/DNA interactions (Gibson, Andrew; Sims, P F G.) trp repressor : The E coli trp Repressor Chime Movie (Lawson, Cathy) Top 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 trpR : The E coli trp Repressor Chime Movie (Lawson, Cathy) trypsin inhibitor : Molecular Science Lab (Oberholser, Karl) trypsinogen-BPTI : Molecular Science Lab (Oberholser, Karl) tryptophan : The E coli trp Repressor Chime Movie (Lawson, Cathy) Top 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 Tryptophan Repressor : Online Macromolecular Museum (Marcey, David; Students at California Lutheran University; Students at Kenyon College) tubulin : FtsZ, a prokaryotic cell-division protein and tubulin homologue (McCool, Gabriel J.) tutorials on molecular structures : Molecular Models for Biochemistry at CMU (McClure, William) Type II restriction endonuclease : BamHI Restriction Endonuclease (at The Online Macromolecular Museum) (Silva, Nathan; Leslie, Kenneth; Marcey, David) Top 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 tyrosine kinase : Explore the c-Src tyrosine kinase (Engen, John R; Superti-Furga, Giulio) tyrosine phosphatases : Protein Tyrosine Phosphatase PTP1B (at The Online Macromolecular Museum) (Silva, Nathan; Marcey, David) U1A : Biomodel (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish) U1A Spliceosomal Protein (at The Online Macromolecular Museum): Cross-indexing terms: RNA splicing; Splicesomal Protein; snRNP This Chime-based exhibit examines the binding of U1A protein to both the U1 snRNA in the U1 snRNP and to the 3' untranslated region of the mRNA that encodes the U1A protein Author: Marcey, David Submitted by: the author (Entry 111) Submitted on Jun 18, 2001 Last revised on Jun 22, 2001 Top 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 universal joint, molecular: flagellar hook : Flagellar Hook, Bacterial A Molecular Universal Joint (Martz, Eric) Valence-Shell Electron-Pair Repulsion Theory (VSEPR) : Web-Based Chemical Investigations (Bragin, Victoria (Vicki)) Van der Waals forces : Chemical Bonds and Protein Structure (at The Online Macromolecular Museum) (Marcey, David) van der Waals interactions, finding : NonCovalent Bond Finder (NCBF) (Martz, Eric) Top 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 van der Waals surface : Accessible, molecular and Van der Waals surfaces explained (Krieger, Elmar) Viagra : The Rational Basis of Drug Design (Walters, D Eric) vibrational modes, infrared spectra, animated : Infrared spectra, animations of vibrational modes (Motyka, Eric; Lahti, Paul; Lancashire, Robert J.) Viral Antigens : Online Macromolecular Museum (Marcey, David; Students at California Lutheran University; Students at Kenyon College) Top 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 Viral Antigens (at The Online Macromolecular Museum): Cross-indexing terms: HIV gp120; influenza hemagglutinin; flu virus; hemagglutinin, influenza This Chime-based exhibit concerns the structure/function/variability of two viral spike antigens, hemagglutinin of the human influenza virus, and glycoprotein 120 (gp120) of the human immunodeficiency virus (HIV-1) Authors: Mazur, Eric; Marcey, David Submitted by: Marcey, David (Entry 117) Submitted on Jun 18, 2001 viral protease : HIV-1 Protease (at The Online Macromolecular Museum) (Mana, Miyeko; Marcey, David) virus capsid structure : SV40 capsid structure and assembly (Welte, Stefan) virus peptides, binding to MHC : Major Histocompatibility Complex (Martz, Eric) Top 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 vmd : Structural Alignment Program for Proteins (Gille, Christoph) von Willebrand factor : Structural Biochemistry of Blood Coagulation (Walters, D Eric) VP1 : SV40 capsid structure and assembly (Welte, Stefan) Water : Molecule of the Month/University of Bristol (May, Paul (editor)) Water : BioMolecular Explorer 3D: Resources for High School Biology (Reichsman, Frieda; Eric Martz) Top 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 Water Simulation: Cross-indexing terms: theoretical simulation of water; simulation, theoretical, water; lesson plan; Chime At MolviZ.Org: A theoretical simulation (done with MDL Sculpt) of 10 water molecules assembling into a compact, hydrogen-bonded network Available as saved animations viewable in Chime, and as a morph for Protein Explorer Ten questions are provided for students about the final hydrogen-bonded droplet Author: Martz, Eric Submitted by: the author (Entry 153) Submitted on Sep 12, 2004 Last revised on Oct 3, 2004 Watson-Crick base pairing and hydrogen bonding : DNA Structure (Martz, Eric) (English, German, Portuguese, Spanish) Watson-Crick base pairing and hydrogen bonding : DNA Structure (with Jmol) (Herraez, Angel; Martz, Eric) Web-Based Chemical Investigations: Cross-indexing terms: organic chemistry; Valence-Shell Electron-Pair Repulsion Theory (VSEPR); cycloalkanes; isomerism, constitutional; stereoisomerism; lesson plans Interactive tutorials in organic chemistry and biochemistry using Chime Organic chemistry modules include • Molecular Geometry and the Valence-Shell Electron-Pair Repulsion Theory • Cycloalkanes: A Structural Study • Constitutional Isomerism • Stereoisomerism Biochemistry modules are listed individually under Bragin in the author index These tutorials use a discovery-based approach to learning concepts Author: Bragin, Victoria (Vicki) Submitted by: the author (Entry 61) Submitted on Aug 17, 2000 Last revised on Mar 19, 2001 WXXXR motif : Cytochrome P450 3D structures page (Nelson, David) Top 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 XdomView: A Chime-based Graphical Tool for Protein Domain and Exon Position Visualization: Cross-indexing terms: domain; CATH; SCOP; DALI; FSSP; MMDB; NCBI; ExInt; BLAST; intron; NUS; Singapore; protein; PDB; structural domain; gene; gene evolution; intron evolution; strucuture; 3DEE; exon; intron XdomView (Version 2.1) A Chime-based Graphical Tool for Protein Domain and Exon Position Visualization XdomView is a chime-based visualization tool that maps the domain boundaries of the input PDB chain, obtained from protein structure classification databases (CATH, SCOP, NCBI, 3DEE and DALI) to its tertiary structure It also runs BLAST2 for the input PDB chain sequence against all protein sequences in the ExInt* database and maps the intron positions and phases of aligned search results on the input protein's 3D structure Xdom is a useful visualization tool for scientists working on gene and protein evolution and structural modeling and classification Enlarged image Contact Details : Gopalan Vivek, Dr Tan Tin Wee, Dr Shoba Ranganathan Bioinformatics Centre Department of Biochemistry National University of Singapore *ExInt - Repository of intron positions, phase and protein sequences of all multi-exonic eukaryotic genes available in GenBank 122 Authors: Gopalan, Vivek; Shoba Ranganathan; Tan Tin Wee Submitted by: the author (Entry 134) Submitted on Jun 10, 2002 XYZ files used for infrared vibrations : Infrared spectra, animations of vibrational modes (Motyka, Eric; Lahti, Paul; Lancashire, Robert J.) XYZ format animation : Thermal motion of alpha helix (Cachau, Raul E.) YASARA : Accessible, molecular and Van der Waals surfaces explained (Krieger, Elmar) Top 3-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z Yeast GAL4 Protein : Structures for Molecular Biology (McClure, William) Z-DNA : Biomodel (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish) Z-DNA : DNA Conformers (at The Online Macromolecular Museum) (Marcey, David) Zif : Molecules and Structures Homepage (Gasser, Charles) zif268 : The Zinc Finger: A Protein Domain that Binds Specific DNA Sequences (Bruist, Michael) Top 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 Zif268 zinc finger : Structures for Molecular Biology (McClure, William) Zinc Binuclear Clusters: Cross-indexing terms: transcription activator; zinc finger; BioEditor Zinc binuclear clusters are motifs found in transcriptional regulatory proteins in fungi An early zinc binuclear cluster was originally thought to be similar to previously described zinc fingers, with four cysteines forming a tetrahedral zinc binding site Subsequent structural studies strated that the zinc binuclear cluster consists of cysteine residues that are bound to two zinc atoms This documentary includes text, images, sequence and structural data and molecular visualizations to describe representative members of this family It is presented in the BioEditor software package Author: Craig, Paul Submitted by: the author (Entry 151) Submitted on May 16, 2004 zinc finger : Biomodel (Herraez, Angel; Lopez-Lopez, Jose Ramon) (Spanish) zinc finger : The Zinc Finger: A Protein Domain that Binds Specific DNA Sequences (Bruist, Michael) zinc finger : Zinc Binuclear Clusters (Craig, Paul) zinc fingers : Chime Square (Niederhoffer, Eric) zinc fingers : Protein/DNA interactions (Gibson, Andrew; Sims, P F G.) Top 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 Zyban : Molecule of the Month/University of Bristol (May, Paul (editor)) Top 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 953 total subject cross-indexing terms Visitor-Maintained Index programming by Trevor D Kramer ... BioMoleculesAlive.Org: Cross-indexing terms: ASBMB; curriculum resources for biochemistry Features free, downloadable, peer-reviewed educational resources including Software, Visual Resources, Curriculum Resources, ... constructing new tutorials and websites with Chime are gathered in this section of the World Index of Molecular Visualization Resources This separates them from the present section, which is for "Ready... Biochemistry of Blood Coagulation (Walters, D Eric) Histrionicotoxin : Molecule of the Month/University of Bristol (May, Paul (editor)) HIV : The Rational Basis of Drug Design (Walters, D Eric) HIV : BioMolecular