World Index of BioMolecular Visualization Resources

Biochemical Structure Tutorials

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  3D Periodic Table of Radii:
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.

  3D Periodic Table of Radii (using Jmol):
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.     

  70S Ribosome Architecture:
Overview of the 70S bacterial ribosome crystal structure and a Chime animation of steps in translation.
PDB ID codes: 1gix.pdb and 1giy.pdb    
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  Accessible, molecular and Van der Waals surfaces explained:
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.

  AHo's Amazing Atlas of Antibody Structure:
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.

  Alkaline phosphatase:
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

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  Amino Acid Identification Quiz:
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.

  Amino Acid Quizzer:
At MolviZ.Org: The wireframe of a small protein is shown in Chime. Each student is assigned a residue number or range. When the number(s) are entered, Chime automatically zooms in to show atomic detail of the amino acid(s) as ball and stick, CPK-colored (color key is provided). Students can then answer questions posed by the instructor such as amino acid identity, side-chain properties, and which of two amino acids is closer to the N terminus. Lesson plan (sequence key is available to instructors on request). Downloadable for off-line use, local installation or modification.

  Amino Acid Structure Quiz:
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.

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  Animations on subjects of Structural and Metabolic Biochemistry:
Chime-based tutorials on protein secondary, structure, hemoglobin and electron-transfer complexes. More will eventually follow.

  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 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.

  Antibody Recognition of Antigen (at The Online Macromolecular Museum):
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.

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

  B-Form Deoxyribonucleic Acid (DNA):
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.

  Bacteriorhodopsin:
A one-page Chime display of nine recent bacteriorhodopsin structures and links to the PubMed entries for the structure references.

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  BamHI Restriction Endonuclease (at The Online Macromolecular Museum):
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.

  Biomodel - in English:
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-1: covers the structure of proteins, nucleic acids and their complexes. 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 and further models of H-bonded water.

  BioMolecular Explorer 3D: Resources for High School Biology:
BioMolecular Explorer 3D is a website designed to provide high school teachers with interactive 3D structures of biologically significant molecules that fit in high school biology curricula.

The following resources are available at BioMolecular Explorer 3D:
  1. Links to software for viewing and exploring molecules in 3D
    • download the software
    • follow our instructions for installing it
  2. Pre-selected biomolecules that fit well in a high school biology curriculum
    • each molecule is placed in its biological context with a brief description
    • each molecule is linked to an interactive 3D display (assuming prior installation of software)
  3. Assistance with lesson planning
    • each molecule is linked to background information specially selected for HS teachers
  4. Access to additional molecules
    • we show you where to find many other biomolecular 3D displays and tutorials

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  Biomolecular Structures:
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.

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

  BioMoleculesAlive.Org:
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.  
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  Carboxypeptidase A - Three Exercises with Chime:
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.

  Catalase (at The Online Macromolecular Museum):
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.

  Chemical Bonds and Protein Structure (at The Online Macromolecular Museum):
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.

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  Chemie und Internet am Gymnasium:   (German )
Lernumgebungen mit CHIME und Skriptsteuerung:

  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.

  Chime and Jmol Files:
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.

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  Chime Square:
"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.

  Chime: Great Sites:
One of the most extensive lists of annotated links to diverse Chime sites. Organic chemistry tutorials and sites are especially well represented here. Includes several sources of small "molecules" (atomic coordinate or PDB) files.

  ConSurf Server for the Identification of Functional Regions in Proteins by Surface Mapping of Phylogenetic Information:
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.

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  Course Home Page for "Computer Applications in Biotechnology":
"Computer Applications in Biotechnology" is a project-based class in which students create interactive tutorials using RasMol and Chemscape Chime. There are many links to examples of student projects. For example, one class project involves illustrating NMR spectra of amino acids and nucleotides using interactive Chime models.

  Cro Repressor of Temperate Bacteriophages (at The Online Macromolecular Museum):
Cro, a repressor protein of temperate bacteriophages (e.g. lambda, 434, P22), works in opposition to the phage's repressor to control the genetic switch that determines whether a lytic or lysogenic cycle will follow infection. This Chime-based exhibit explores the structure of cro.

  Cytochrome P450 3D structures page:
This site provides a 3D structure primer on cytochrome P450. The initial page includes 37 images made as RasMol scripts and embedded in a Chime template for interactive viewing. These images start at the bare PDB output for P450 cam (CYP101) and move to more and more detail on P450 structure. This includes a tour of the conserved motifs in the more than 2500 P450 sequences known. Each motif is visited with the intent of understanding what the conserved residues are doing in the structure of the protein. This is rather like walking around in a big version of the molecule to see how it is put together. This approach frequently leads to charge pairs critical to the protein fold and sometimes to charge triads. Some images are from CYP2C5, a mammalian P450 with motifs absent in the bacterial P450s. The 3D pages are part of a larger Cytochrome P450 homepage, in operation since 1995 at this same URL. Page created Nov. 2002.  
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  DNA Conformers (at The Online Macromolecular Museum):
This Chime-based tutorial compares the essential structural features of A-, B-, and Z-DNA.

  DNA Polymerase Beta (at The Online Macromolecular Museum):
DNA polymerase Beta (pol B) is a eukaryotic DNA polymerase studied most extensively in vertebrate systems. Like other DNA polymerases, pol B is responsible for adding new nucleotides to a growing chain by catalyzing a nucleotidyl transfer reaction. This Chime-based exhibit explores structural aspects of Pol B catalysis, DNA binding, processivity, and fidelity.

  DNA Polymerase I from Thermus aquaticus:
This chime window presents students with DNA polymerase in the act of adding a nucleotide to a primer. Both the polymerization domain and 3' to 5' exonuclease are depicted. The template and primer strands along with the incoming nucleotide can be viewed in various modes. There is a zoom into the active site enabling one to clearly see how an SN1 reaction will add the nucleotide to the primer DNA strand. The window functions as a tutorial in which several questions are posed, with answers available with a click. The coordinates have been modified so that actual substrates rather than inhibitors are seen on the enzyme.

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  DNA Polymerase III-Beta Subunit (at The Online Macromolecular Museum):
The beta subunit of DNA pol III (E. coli)provides for the remarkable processivity of the holoenzyme during replication. The subunit is a ring-shaped clamp that embraces DNA in a central 35 angstrom hole and tethers the remainder of pol III to the template. This Chime-based exhibit explores the structure and function of the polIII beta subunit.

  DNA Polymerase of Bacteriophage T7 (at The Online Macromolecular Museum):
The bacteriophage T7 DNA replication complex is a good model system for the study of the mechanism of DNA synthesis because it consists of relatively few proteins. This Chime-based exhibit focuses on how processivity is maintained during DNA synthesis, on how metal cations are involved in nucleotide addition, and on how T7 DNA polymerase recognizes specific nucleotides.

  DNA quizzer:
A lab exercise in DNA structure. Students select a short DNA sequence by number & must deterine its nucleotide sequence.

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  DNA Structure:   (English, German, Portuguese, Spanish )
At MolviZ.Org: Chime images of a 17-base-pair DNA double helix. This is not a self-contained tutorial, but rather a supplement to a text or class on DNA structure. Buttons which highlight features of the DNA may be pressed in any order, and their actions depend on which buttons were pressed earler. For example, [Bases] followed by [Spacefill] spacefills all the base pairs (but not the backbone), whereas [GC] followed by [Spacefill] spacefills the single GC base pair. Four pages emphasize (1) base pairs and hydrogen bonding, (2) the code, (3) strands and helical backbone, and (4) ends and antiparallelism. A simple animation of base-by-base replication is included. The nonlinear/random button interface is unique among Chime presentations on the web. Downloadable for off-line use, local installation or modification. Last version July 2002 is compatible with Windows Internet Explorer, and has other enhancements. You will probably prefer to use the more up-to-date version that uses Jmol (see below) and is compatible wiith all modern browsers.

Also available in German, Portuguese, and Spanish.

  DNA Structure:   (English, Italian )
Chime-based tutorial including fundamentals of backbone structure, basepairing and helix stabilization. Detailed look at sugar and base configuration/numbering schemes, and strand direction. References to figures in Stryer's Biochemistry, 4th edition. Implementation includes text, movies, and help. Available in Italian courtesy of Giuseppe Striccoli.

  DNA Structure (at The Online Macromolecular Museum):
This Chime-based exhibit explores the structures of the B-DNA polymer and B-form double helix.

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  DNA Structure (with Jmol):   (English, Spanish, German, Portuguese, French, Romanian, Italian )
Adaptation of the existing "DNA Structure" tutorial by Eric Martz (see above); this updated version uses Jmol instead of Chime. Compatible with most modern browsers and operating systems (including MacOSX and Linux). Needs Java installed. Also available in Spanish, Portuguese, French, German, Romanian and Italian.

  DNA Topoisomerase I (at The Online Macromolecular Museum):
E. coli DNA Topoisomerase I is responsible for the relaxation of negative supercoils in the bacterial chromosome. Topoisomerase I has also been implicated in knotting and unknotting DNA and in linking complementary rings of single-stranded DNA into double-stranded rings. The focus of this Chime-based exhibit is the structure-function relationships of the 67K, N-terminal fragment of Topoisomerase I.  

  Erythropoietin - EPO Receptor Complex (at The Online Macromolecular Museum):
Erythropoietin (EPO), a cytokine hormone, is responsible for the regulation of red blood cell production. EPO is a glycoprotein produced primarily in the the kidney. Secreted EPO (165 amino acids) binds to EPO receptors on the surface of bone marrow erythroid precursors, resulting in their rapid replication and maturation to functional red blood cells. This Chime-based exhibit explores EPO and EPO Receptor structure and binding.

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  Estrogen Receptor Structures & Function:
An "Overview" provides a brief introduction to the estrogen receptor (ER) and its functions, including literature citations and WWW links. The Chime pages show ERa and ERb as dimers and focus on the ligand specificity and conformational changes that accompany agonist or antagonist binding to the ligand-binding domain (LBD). The LBD complexes include the agonists: estradiol, diethlystilbestrol, and genistein; the antagonists shown are: raloxifene and tamoxifen. Differences between the ERa and ERb complexes are shown separately and as superimposed (aligned) models. The ER DNA-binding domain (DBD) complex with an ERE is also shown. Linked pages show small molecule models of the above ligands and several other estrogens and steroids.
PDB ID codes: 1ERE, 1ERR, 3ERD, 3ERT, 1A52, 1QKM, 1QKN, 1HCQ.

  Estructura de Macromoleculas:   (Spanish )
CHIME-based visualization of small biomolecules and elements corresponding to the different structural levels of proteins and DNA (primary, secondary, supersecondary, tertiary and quaternary structures). RASMOL scripts translated to Spanish (from the RASMOL home pageand UMASS resources page) Links related to biological macromolecular structure. This page is thoroughly used for academic teaching.
Visualizacion en CHIME de biomoleculas pequenas y de elementos correspondientes a diferentes niveles estructurales de proteinas (primario, secundario, supersecundario,terciario, cuaternario) y de DNA. "Scripts" de Rasmol a partir de la "home page" deRASMOL y la pagina de recursos de UMASS traducidos al castellano. Enlaces a bases de datos de estructura de macromoleculas biologicas. Esta pagina es muy adecuada para clases academicas.

  Everything You Ever Wanted to Know about Sweeteners:
Contains information about commonly used high potency sweeteners: acesulfame, aspartame, cyclamate, saccharin, and sucralose. Included for each sweetener are molecular formula, molecular weight, chemical structure, chemical and commercial names, Chime structures, stories about the discovery of sweeteners, and concentration-vs.-response data.

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  Explore the c-Src tyrosine kinase:
A chime-based, tutorial page of the structure of the tyrosine kinase c-Src. Buttons allow the user to selectively highlight important domains and residues critical for regulation of Src and its family members. A link in the page takes you to more information about c-Src, its properties, and regulation.

  Exploring Glyceraldehyde-3-phosphate dehydrogenase:
This page explores the heirarchy of protein structure. Glyceraldehyde-3-phosphate dehydrogenase is a homotetramer. The arrangement of the four subunits is observed. An animation goes from the space-filling tetramer to a single subunit, which is then converted to a ribbon cartoon. It is seen that each domain binds one substrate. The secondary features that comprise the NAD+ binding domain are presented. These can be isolated or seen in contect of the full domain. Side chains can be toggled on and off.  

  Fibronectin (at The Online Macromolecular Museum):
Fibronectin (FN) is involved in many cellular processes, including tissue repair, embryogenesis, blood clotting, and cell migration/adhesion. FN exists in two main forms: 1) as an insoluble glycoprotein dimer that serves as a linker in the extracellular matrix, and; 2) as a soluble disulphide linked dimer found in the plasma. This Chime-based exhibit exlores the structure-function relationships of FN.

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  Flagellar Hook, Bacterial -- A Molecular Universal Joint:
Animations of the rotation of the bacterial flagellar hook, based on a crystal structure of the monomer, 121 copies of which were assembled into a cryo-EM structure of the hook, and rotated by molecular dynamics simulation. Based on work by Samatey et al. in the groups of DeRosier and Namba, published in Nature 431:1062, October 2004.

  FtsZ, a prokaryotic cell-division protein and tubulin homologue.:
A detailed tour of FtsZ structure, including a sequence alignment, fluorescence a time-lapse movie of the protein in dividing cells, with over 50 views in Chime. The GTP-binding motif and structural alignment of FtsZ and tubulin are featured. This presentation is a prototype within Protein Explorer 1.0. This means you can use the full capabilities of Protein Explorer to manipulate any view in the presentation.  

  G Proteins (Trimeric): Molecular On/Off Switches, at Biochemistry in 3D:
Chime-based tutorial on trimeric G proteins including 3 switch regions near the GTP/GDP-binding site, detailed look at the conformational changes upon GTP hydrolysis or GDP/GTP exchange, dissociation of the alpha chain from the beta/gamma chains and its control by switch regions. References to figures in Lehninger's Principles of Biochemistry (Lehninger, Nelson & Cox), 3rd edition. Implementation includes pop-up detail boxes, movies, color keys, extensive help, busy/idle status indicators, and a powerful interface for self-directed exploration of the tutorial images.

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  Garrett & Grisham Interactive Biochemistry:
The support site for Garrett & Grisham's Biochemistry text, including Chime-based tutorials on the topics listed above.

  Garrett and Grisham Interactive Biochemistry Structure Tutorials:
These structure tutorials support the Garrett and Grisham textbook, and require the Chime plug-in. Students can learn how to use Chime, and see tutorials on nucleic acids, serum albumin, myoglobin, the class I major histocompatibility complex (MHC I), and the alpha-helix.

  GFP (Green Fluorescent Protein):
structural biology and reaction chemistry of the green fluorescent protein (GFP). uses Chime, gifs, and text in combination. supports use of Chime 1.x or higher. originally designed as a lecture aid, but can be used as a self-guided tutorial as well.  
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  Hammerhead Ribozyme:
This Chime tutorial includes basic aspects of RNA secondary structure, an SN2 reaction animation, a close look at catalysis, ribozyme reaction intermediates, and an animation of ground, intermediate, and product structures. Smooth transitions between views show their relationships clearly. The interface is easy to use for students and novices, but advanced users can modify the images with menus, or enter Chime commands.

  Hemoglobin:
At MolviZ.Org: A tutorial on hemoglobin in Chime including an introduction to stick, ball and stick, spacefill renderings, peptides and backbones, basic hemoglobin tetramer structure, heme, iron, histidine and oxygen binding to iron, secondary structure, zoom to one alpha helix and its hydrogen bonds, amphipathicity of helices, hydrophobic interior and polar surface of each monomer, sickle hemoglobin, its mutation and how that causes polymerization. Buttons can be pushed in any order yet always give the same images. Font size can be dymanically changed for large audiences. The utilities menu enables recentering, atom identification, measuring distances, and changing background color from black to white for printing. Downloadable for off-line use, local installation or modification.

  Hemoglobin I:
A lecture-oriented chime 'slide show' about hemoglobin. Buttons show particular views (these must usually be played in order) and a caption appears in the lowest frame. This one shows hemoglobin - you can switch from deoxy to oxy & back in both spacefill & backbone views. You can alse see the 4 chains & heme. It then turns to b-globin & shows secondary structure as well as examples of an ionic bond, a hydrogen bond, and a hydrophobic interaction.

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  Hemoglobin II:
A lecture-oriented chime 'slide show' about hemoglobin. Buttons show particular views (these must usually be played in order) and a caption appears in the lowest frame. This one shows two mutants of hemoglobin & their effects:

  Hemoglobin-S Polymerization Binding Site:
This is a draft demo of the hemoglobin-S polymerization binding site that results in sickle cell anemia due to a point mutation. The demo hi-lites the different hemoglobin chains, the heme groups within them, the point mutation, and the hydrophobic pocket in separate hemoglobin tetramers that bind to it such that polymerization occurs. The intended audience is high school advanced biology students.

  HhaI DNA Methyltransferase (at The Online Macromolecular Museum):
Methyltransferases are employed in restriction-modification and mismatch repair systems in prokaryotes, and have been implicated in many molecular processes in eukaryotes including regulation of gene expression, genomic imprinting, DNA repair, mutagenesis, and chromatin organization. HhaI DNA methyltransferase is a prokaryotic m5c-methyltransferase that recognizes the 5'-GCGC-3' sequence in double stranded DNA and methylates the first cysteine of the recognition sequence. This Chime-based exhibit explores the structure-function relationships of HhaI.

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  Highlights of biochemistry: molecular structures made visible.:   (English or German )
Interactive Chime scripts on selected topics of biochemistry - enzyme structures with special features up to reaction pathways.
Biochemie zum Ansehen: molekulare Strukturen vom Atom zum Makromolekuel:Interaktive Chime Skripte zu biochemischen Themen - von Enzymstrukturen mit Besonderheiten zu Reaktionswegen.

  Hin Recombinase (at The Online Macromolecular Museum):
Hin recombinase catalyzes a site-specific DNA inversion in the Salmonella chromosome. The recombination event regulates the alternate expression of two flagellin genes, H2 and H1. This Chime-based exhibit explores the structure-function relationships of the recombinase.

  HIV-1 Integrase (at The Online Macromolecular Museum):
The integration of HIV-1 DNA into the host chromosome is achieved by the integrase protein performing a series of DNA cutting and joining reactions. This Chime-based exhibit focuses on the catalytic core domain and minimal DNA binding domain of HIV-1 integrase.

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  HIV-1 Nef Protein (at The Online Macromolecular Museum):
Nef is a viral protein that interacts with host cell signal transduction proteins to provide for long term survival of infected T cells and for destruction of non-infected T cells by inducing apoptosis. Nef also advances the endocytosis and degradation of cell surface proteins, including CD4 and MHC proteins. This Chime-based exhibit focuses on the structural features of the Nef core domain that provide for its mutiple functions.

  HIV-1 Protease (at The Online Macromolecular Museum):
HIV-1 Protease (PR) hydrolyzes viral polyproteins into functional protein products that are essential for viral assembly and subsequent activity. This maturation process occurs as the virion buds from the host cell. This Chime-based exhibit focuses on the structure-function relationships of PR.

  HIV-1 Reverse Transcriptase (at The Online Macromolecular Museum):
The enzyme reverse transcriptase (RT) is used by retroviruses to transcribe their single-stranded RNA genome into single-stranded DNA and to subsequently construct a complementary strand of DNA, providing a DNA double helix capable of integration into host cell chromosomes. This exhibit focuses on the structure-function relationships of the HIV-1 RT. The action of some RT inhibitors is examined.

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  How to Create New Chime Tutorials:
At MolviZ.Org: Methods and tools for constructing new tutorials and websites with Chime are gathered in this section of the World Index of Molecular Visualization Resources. This separates them from the present section, which is for "Ready to Use" tutorials.  

  Images of Glycolysis Intermediates:
In a frames format, the reactions of glycolysis are shown as Chime displays of the substrates, products and cofactors. Links to the fermentation fates of pyruvate and to similar displays of TCA cycle intermediates are provided.

  Images of TCA Cycle Intermediates:
In a frames format, the reactions of the TCA Cycle are shown as Chime displays of the substrates, products and cofactors.

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  Immunoglobulin Structure (at The Online Macromolecular Museum):
This Chime-based exhibit provides an introduction to immunoglobulin structure, including tetramer structure, the structure of the immunoglobulin fold, and the structure of the variable region.

  Infrared spectra, animations of vibrational modes:
The IR spectrum of acetophenone is given as an example (rendered by Chime from a data file in the JCAMP format). Clicking on a peak animates the corresponding vibrational mode in a Chime-rendering of the molecule. Links to additional resources detail the methods employed to construct such displays, as well as resources that highlight bonds or atoms corresponding to peaks in MS or NMR spectra, and IR spectra for a series of additional molecules. Downloadable for off-line use, local installation or modification.

  Interactive Quercetin 2,3-Dioxygenase Presentation:
Chime-based presentation of the (crystal) structure of the copper-containing quercetin 2,3-dioxygenase from Aspergillus japonicus. Description of monomer and dimer structure with extensive glycosylation, the active site with substrate and homology with other enzymes.
Script buttons invoke "movies"; in addition general commands can also be executed by clicking a button. Resources (literature, PDB links) included.

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  Introduction to Protein Structure:
This CHIME-enhanced site is meant for beginning biochemistry students. It covers every thing from the acid-base chemistry of the amino acids through the hierarchy of protein structure (i.e. primary to quarternary) much as the typical undergraduate biochemistry textbook does except that "live", interactive CHIME structures are used throughout.

  Introduction to Protein Structure, Part I:
A custom Web-based application which uses a discovery-based approach to examining protein structure. In part I, primary and secondary structures are introduced by analyzing simple polypeptides. This forms the springboard for the analysis of more complex proteins. Visualization employs Chime.

  Isoprenoid Biosynthesis Pathway:
Chime is used to illustrate each step in this pathway, including the conversion of acetyl-CoA to cholesterol and the abundance of intermediate forms that are vectored off for other purposes, including isoprenylated proteins such as rhodopsin kinase.    
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  Lac repressor bending DNA operon:
At MolviZ.Org: Animations of the lac repressor bending its DNA operon when nonspecific binding to DNA converts to specific binding. Several animations that can be viewed in MDL Chime highlight different aspects of the specific binding process. One shows 5 hydrogen bonds forming in the major and minor grooves representing sequence-specific recognition. The animations were saved from Protein Explorer using a linear-interpolation morph, which is provided for direct exploration in Protein Explorer. Questions are provided for students.

  Lac Repressor: Biochemistry in 3D:
An in-depth investigation into the function of this classic bacterial gene regulator. Includes animations showing the binding of lacR to DNA operators, core dimer and tetramer interactions, and structural effects of inducer binding. follow the allosteric effects of inducer binding as they propagate through the core to the headpiece, and affect the interaction between lacR and its operator sites. One of several detailed Chime structure-function tutorials that accompany Lehninger Principles of Biochemistry. All of these tutorials require Chime and Netscape Communicator 4.5-4.79, and use actual structure files from various sources. all tutorials are extensively annotated with text and citations, and offer powerful, user-friendly controls to supplement the Chime animations.

  Large Ribosomal Subunit Tour:
A Chime-based tour of the large ribosomal subunit suitable for college-level classes. Highlights the key features of the large subunit such as the site of peptide bond synthesis and the polypeptide exit tunnel. Demonstrates how the ribosome seems to be a ribozyme and shows one theory on how the chemistry works. Based on the structure of the Archaeal large ribosomal subunit reported in 2000 by Steitz, Moore, and coworkers.

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  Large Ribosomal Subunit Tour for Specialists:
An extensive, Chime-based tour of the Archaeal Large Ribosomal Subunit for specialists. The full tour requires Netscape Communicator (Navigator) 4.5-4.7 but there is a sample tour that covers the key features that works with Chime in other browsers on computers running Microsoft Windows. The full tour interface has been designed with the issues that the large coordinate data files entail in mind. Be aware that you need a good connection to the internet for this to work and not be frustrating. Several of the structure files used in the tour are in excess of 1 Mb.

  Lipid Bilayers and the Gramicidin Channel (Chime version):
At MolviZ.Org: This Chime presentation shows cholesterol, phosphatidyl choline, and then illustrates the assembly of hydrated crystalline bilayer model. Results of two molecular dynamics simulations (by Helmut Heller et al.) are shown, resulting in gel- and fluid-like conformations. Then the gramicidin channel is shown in a hydrated bilayer of phosphatidyl ethanolamine (modeled by Serge Crouzy et al.). Adapted to Chime in 2001 by Angel Herraez from the 1997 RasMol "Movie" Script by Eric Martz. Also available in Spanish. Links are provided for further exploration of these models in Protein Explorer. Now also available using Jmol, both in English and Spanish (indexed separately under the same title).

  Lipid Bilayers and the Gramicidin Channel (Jmol version):
This Jmol presentation shows cholesterol, phosphatidyl choline, and then illustrates the assembly of hydrated crystalline bilayer model. Results of two molecular dynamics simulations (by Helmut Heller et al.) are shown, resulting in gel- and fluid-like conformations. Then the gramicidin channel is shown in a hydrated bilayer of phosphatidyl ethanolamine (modeled by Serge Crouzy et al.). Adapted to Jmol in 2005 by Angel Herraez from the 2001 Chime version (by the same author, indexed separately under the same title) and the 1997 RasMol "Movie" Script by Eric Martz. Also available in Spanish.  
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  Macromolecular Visualization Laboratory Exercise:
The tutorial with accompanyng exercises illustrates the kind of questions students can answer with the help of computer modeling. It focuses on analysis of molecular structures and shows how to create images that help to illustrate important features of macromolecules. The tutorial also teaches that biological macromolecules come in very different shapes and sizes.

The tutorial also teaches a few technical skills that are commonly used while working with computer visualization programs. First, it shows some typical capabilities of the visualization programs SYBYL and RasMol. It also teaches about image capture and manipulation programs on SGI workstations, and shows how one can send images created on an UNIX computer to other people.

The tutorial assumes access to modeling programs SYBYL and RasMol. The tutorial is part of a formal coursework for biochemistry majors at UCSB.

  Magnesium Adenosine Triphosphate (MgATP) Binding to an Enzyme:
This page illustrates how an enzyme binds specifically to a substrate using dethiobiotin synthetase from E. coli. The initial space-filling view shows ATP buried on the surface of an enzyme. An animation then zooms into the active site as all protein residues not binding ATP are removed. The hydrophobic interactions, hydrgen bonding, and ionic interactions can be color coded. Monitors (lines) indicating hydrogen bonds and salt bridges can be toggled on and off. A simple rigid body animation shows how ATP might move into this site from solution.

  Major Histocompatibility Complex:
At MolviZ.Org: A tutorial on MHC structure in Chime including an introduction to stick, ball and stick, spacefill renderings, peptides and backbones, disulfide bond renderings, MHC class I secondary and tertiary structure, beta-2 microglobulin, CD8-binding site, papain cleavage site, the peptide-binding cleft, Sendai nucleoprotein nonamer and vesicular stomatitus virus nucleoprotein octamer binding to H-2Kb with comparison of their T-cell epitopes. MHC class II secondary and tertiary structure and peptide binding (HLA-DR1 with influenza hemagglutinin 13-mer). Buttons can be pushed in any order yet always give the same images. Font size can be dymanically changed for large audiences. The utilities menu enables recentering, atom identification, measuring distances, and changing background color from black to white for printing. A list of questions is provided which can be printed and handed out to a class as a focus worksheet (lesson plan). Downloadable for off-line use, local installation or modification.

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  Major Histocompatibility Complex:
This Chime tutorial is a comparative exploration of Class I and II MHC proteins and their bound peptdes. Major similarities and differences are elucidated in side-by-side comparisons (using two Chime windows next to each other). Each class of MHC is also explored in depth individually. Close attention to binding pockets and specificity of binding. Use of surface representations to illustrate binding clefts and anchor pockets. Smooth transitions between views show their relationships clearly. The interface is easy to use for students and novices, but advanced users can modify the images with menus, or enter Chime commands.

  Membrane Channel & Pump Structures:
An index table of structures for biochemistry courses. PubMed entries and Chime displays of the structures can be viewed by following the links provided. (PDB ID) for the structures displayed are shown above.

  Molecular Electrostatics with PMV:
potential Covers Computation and Visualization of Electrostatic Potential in PMV.
  1. Quickstart Describes minimal steps needed to run APBS and visualize the results.
  2. Potential Isocontours Explains how to display isocontours of an electrostatic potential.
  3. APBS Setup widget How-to change parameters.
  4. Add-on Creating animated images for presentation or Web pages.

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  Molecular Models for Biochemistry at CMU:
Index page with links to tutorials and quizzes that are based on Chime and RasMol images of the molecules and macromolecules found in biochemistry. They are intended to complement standard biochemistry texts where more explanation is provided, but where interactive 3-D images of the molecules are not available. Links to various pages used in courses at Carnegie Mellon University.

  Molecular Movies - A Portal to Cell and Molecular Animation:
Animations at this site are, for the most part, sophisticated cartoons, rather than the atomic resolution images more common at molvisindex.org. As a result, these animations beautifully illustrate processes at a larger scale that would be difficult to convey as well with atomic resolution models. MolecularMovies.Org gathers links to such animations by diverse authors and institutions, including

  Molecular Science Lab:
Contains exercises that use Protein Explorer to study the structure and function of proteins. Most of the exercises consist of Presentations in Protein Explorer, and some give suggestions of ways to use PE to investigate the structure of the protein. Illustrations and tips are given on the use of PE. Major topics covered are introduction to fibrous and globular proteins, myoglobins, mitochondrial respiratory complexe III.

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  Molecular Visualization Resources for Project VISM:
VISM is an NSF-funded program to promote the use of computer visualization resources in teaching science and math, especially for 6-12 students. This page is the VISM resource page for using RasMol and Chemscape Chime to teach Geology, Earth Science, Environmental Sciences and other Physical Sciences, as well as Biology and Chemistry. The page is under continual construction. Currently, there is one model lesson plan for "the Bowen's Reaction Series." Other lesson plans are under development. We are interested in developing a repository of pdb files for molecules related to physical sciences. However, there will also be lesson plans for Biology and Chemistry.

  Molecule of the Month/Oxford University:
Short overviews of the history and chemistry of diverse molecules, written by various authors. In each month, a different molecule is featured at each of the MOTM sites. Chime is often employed.

  Molecule of the Month/University of Bristol:
Short overviews of the history and chemistry of diverse molecules, written by various authors. In each month, a different molecule is featured at each of the MOTM sites. Chime is often employed.

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  Molecules and Structures Homepage:
Lead-in page to structures of amino acids in Chime format, Chymotrypsin tutorial in chime format, and set of pages showing a varitey of regulatory transcription factors and TATA-binding protein in Chime format with buttons for different views. Compare structures of B- and X-DNA.

  Molecules for Modern/Cell Biology:
An index table of figures in common textbooks for introductory biology or cell biology courses where molecular structures are pictured. Chime displays of the structures can be viewed by following the links provided.

  Molecules of the Month/Imperial College:
Short overviews of the history and chemistry of diverse molecules, written by various authors. In each month, a different molecule is featured at each of the MOTM sites.

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  MolUSc - Molecules pour un Usage Scholaire:   (French )
MolUSc is a Chime-based web resource in French (MolUSc is the French acronym for Molecules for Scholarly Use). It may be thought of as a simpler Protein Explorer. Its aim is to give students full access to Chime possibilities, without needing to know any RasMol script commands.
In MolUSc all commands are available in easy-access menus. MolUSc allows surface displays, selections from sequences, comparing two molecules... MolUSc works with Netscape Navigator and even better in Internet Explorer. MolUSc can be downloaded and used freely for non commercial purposes.

MolUSc est un programme de manipulation de molecules base sur le plug-in Chime (MolUSc signifie modelisation de Molecules pour un Usage Scolaire). L'objectif de MolUSc est de donner l'acces aux eleves a toutes les possibilites de Chime, au travers d'une interface conviviale, sans avoir a taper d'instructions de commande. MolUSc permet d'afficher des surfaces, de faire des selections a partir des sequences, de comparer deux molecules,... MolUSc fonctionne avec Netscape Navigator mais aussi avec Internet Explorer (meme mieux). MolUSc peut etre telecharge, et utilise librement dans un but educatif et non commercial uniquement.

  MolviZ.Org:   (English, Spanish, German, Portuguese )
MolviZ.Org is easy to remember for accessing diverse tutorials and molecular visualization resources listed alphabetically elsewhere in this index, such as DNA Structure, Hemoglobin, Antibody, Major Histocompatibility, Lipid Bilayers and Channels, vibrations in IR spectroscopy, simulation of water forming hydrogen bonds, the Protein Explorer, Protein Morpher, Atlas of Macromolecules, Noncovalent Bond Finder, Toobers in Science Education, History of Visualization of Biological Macromolecules, Knots in Proteins, and methods for creating web pages using MDL Chime. One thing that distinguishes MolviZ.Org from other collections of molecular visualization resources is that all of the tutorials at MolviZ.Org are downloadable.

  Morpher, Protein:
At MolviZ.Org: Morphs of conformational changes, featuring recoverin, a calcium-activated myristoyl switch and its EF-hands binding/losing calcium. Also offered are undocumented morphs of calmodulin binding calcium, then peptide; influenza hemagglutinin low pH change; integrin CD11b MIDAS domain putative affinity increase for ligand; and cAMP kinase binding regulatory peptide. Introduction addresses the purpose of morphing, and the pros and cons of linear interpolation vs. plausible intermediate modeling. Morphing methods are detailed. Downloadable for off-line use, local installation or modification.

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  MutH (at The Online Macromolecular Museum):
The MutH protein of Escherichia coli, a weak endonuclease, is one enzyme of a multimeric complex that works to repair DNA base mismatches (with the exception of C-C pairs) and small insertion or deletion mismatches in strands differing in up to four nucleotides. This Chime-based exhibit explores the structure/function relationships of this DNA repair protein.

  MutS DNA Repair Protein (at The Online Macromolecular Museum):
The MutS protein of E. coli is responsible for repairing mismatched base errors that occur in DNA replication. MutS increases the fidelity of DNA replication 100-1,000 times. This Chime-based exhibit explores the structure-function relationships of MutS.  

  Nitrogen Regulatory Protein C (at The Online Macromolecular Museum):
Nitrogen Regulatory Protein C (NtrC) is a positively acting bacterial transcription factor that is involved in regulating the metabolism of nitrogen. This exhibit explores the structure-function relationships of the N-terminal receiver domain of NtrC. Special attention is paid to the conformational changes of the receiver domain induced by phosphorylation.

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  NonCovalent Bond Finder (NCBF):
At MolviZ.Org: The NonCovalent Bond Finder is a Chime-based tool for finding and displaying the atoms closest to any moiety of interest ("target") in any molecule. After loading your molecule and selecting the target atom or atoms, simply pressing a button labeled "Find" displays the atoms within 2.5 Angstroms of the target. Repeated presses of the "Find" button move out in 0.1 Angstrom increments, highlighting newly found atoms with dot surfaces. The starting distance and step size are configurable. The "find only" and "don't find" options enable, for example, only hydrogen bonds, or only hydrophobic interactions to be visualized in a given cycle. A detailed tutorial is provided, using the binding of a nonapeptide to a major histocompatibility protein as an example. Here is a snapshot of the NCBF in action. Downloadable for off-line use, local installation or modification.

  Noncovalent Interactions in Proteins:
A Chime-based web page dedicated to the importance and prevalence of pi-type interactions in proteins and protein-ligand complexes. Specific noncovalent interactions are shown that stabilize the structure of protein systems. A special emphasis has been placed on pi-type interactions such as cation-pi interactions between aromatic and basic amino-acid side chains and face-to-face and face-to-edge interactions between two aromatic side chains. All the interactions shown were found by biochemistry students who participated in molecular visualization class projects.

  Nucleic Acid Structure Tutorials:
Chime-based tutorials of the following structures:Comparison of A, B, and Z DNA. Side-by-side comparison of structures, highlighting stacking, grooves, and base-pairs. Based on Science 216: 475-485.[Medline Abstract]
tRNA structure Highlights tertiary interacions and base-stacking of tRNA. Based on Science. 194, 796-806. [Medline Abstract]
Nucleotide numbering help. In case you have trouble keeping up with the atoms of the nucleotide structures.
GroupI intron ribozyme - Full Structure. Catalytic self-splicing RNA. Includes new tertiary interactions: adenosine platform, the tetraloop receptor,the adenosine platform, the ribose zipper, and the tight turn. Based on Science282:259-264 [Medline abstract]
Hammerhead Ribozyme. Small catalytic RNA, showing conserved residues, U-turn motif near active site. Based on Nature 372, 68-74.[Medline Abstract]
MATa1/alpha2-DNA Complex Shows DNA bending, protein-protein interaction, protein-DNA contacts, water mediated H-bonds. Based on Science 270, 262-269. [Medline abstract]
Nucleosome core particle. Shows the "histone fold", which holds protein core together and interacts with DNA. Non sequence-specific protein-DNA interactions.Based on Nature. 389, 251-60.[Medline abstract].
U1A Protein-RNA structure RNP-domain binding to RNA. Major groove binding at end of RNA helix. Induced fit. Based on Nature. 372, 432-438.[Medline abstract]

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  Nucleotide Identification Quiz:
Quiz in a frames format; the user is required to identify 15 common nucleotides shown as Chime images by name and abbreviation. Answers are provided after each selection, and a running total of correct and incorrect responses is tabulated.  

  Online Macromolecular Museum:
The Online Macromolecular Museum (OMM) is a site for the display and study of macromolecules. The OMM's exhibits are interactive, Chime-based tutorials on individual molecules in which hypertextual explanations of important biochemical features are linked to illustrative renderings of the molecule at hand. The OMM's exhibits are grouped into "halls" based on function.
- Hall of Introductory Exhibits
- Hall of Catalysis
- Hall of Cell Adhesion
- Hall of Membrane Biology
- Hall of DNA Polymerization
- Hall of DNA Recombination, Modification, Repair
- Hall of Signal Transduction and Transcription		 - Hall of Ribonucleoproteins
- Hall of Immunology
- Hall of Virology

  Overviews of DNA & RNA Structure:
Side-by-side Chime displays of DNA and RNA with highlighted G-C and A-T(A-U) base pairs.

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  Oxygen Binding Proteins: Myoglobin and Hemoglobin:
Chime-based tutorial including basics of myoglobin structure and function, interactions with heme, detailed look at hemoglobin's conformational changes with emphasis on the mechanism of R to T state conformational switching. Also includes interaction of hemoglobin with the allosteric regulator BPG, and exploration of sickle cell disease hemoglobin. References to figures in Lehninger's Principles of Biochemistry (Lehninger, Nelson & Cox), 3rd edition. Implementation includes pop-up detail boxes, movies, color keys, extensive help, busy/idle status indicators, and a powerful interface for self-directed exploration of the tutorial images.  

  PDB Lite:
Designed for novices, students, educators, and occasional users, this search interface to the Protein Data Bank has direct links for viewing molecules in "FirstGlance in Chime" and Protein Explorer. PDB Lite's database is updated weekly with new releases. TheProtein Data Bank is the international archive of all published 3D macromolecular structures.

  Porin Proteins (at The Online Macromolecular Museum):
The porin superfamily contains a number of homotrimeric, transmembrane proteins that form water-filled pores across the outer cell membranes of gram-negative bacteria. Porins allow bacterial cells to interact with their environment through the passive diffusion of small, hydrophillic solutes across bacterial membranes. OMPF (outer membrane protein f) is among the most general E. coli porins. Maltoporin, also known as the LamB porin, is among the best studied examples of the substrate-specific porins. It is responsible for the guided diffusion of maltose and maltodextrins. Maltoporin is also one of the many porins that contains a bacteriophage recognition sequence. It was identified as the E. coli receptor for phage lambda before its role in the translocation of sugar was discovered. This Chime-based exhibit explores the structure-function relationships of OMPF and Maltoporin.

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  Protein Architecture at Biochemistry in 3D:
Chime-based tutorial including amino acids (stereochemistry, sidechains and categories, proline vs. structure), peptide bond, sequence, secondary structure (phi/psi angles, alpha helices, beta sheets, turns), hydrogen bonds, tertiary structure (fibrous proteins - kinesin, collagen, silk fibroin), small globular proteins (myoglobin, lysozyme), supersecondary motifs, domains, SCOP, examples of alpha, beta, alpha/beta (mixed or segregated), quaternary structure (hemoglobin, poliovirus, tobacco mosaic virus, binding interfaces). References to figures in Lehninger's Principles of Biochemistry (Lehninger, Nelson & Cox), 3rd edition. Implementation includes color keys, extensive help, and busy/idle status indicators.

  Protein Explorer for Novices:
Choose any molecule, and explore it in Chime. Protein Explorer makes the power of Chime easy to use. The initial molecular image is maximally informative, and is explained for novices by the FirstView screen. The QuickViews menus and buttons enable powerful visualization by novices without use of RasMol-style commands (but Protein Explorer accepts all RasMol commands should you know any). Every operation is explained with color keys where appropriate. Much easier to use yet more powerful than RasMol, Protein Explorer includes MENU options for selection by chain, rendering of surfaces and contact surfaces, hiding portions of the structure, automated tools for distinguishing DNA from RNA, centering, and coloring by ATCGU or hydrophobicity/polarity. The amino acid or nucleotide sequence can be clicked to locate residues in the 3D structure (Seq3D). Snapshots offer a quick preview. See also Advanced Protein Explorer which has many more capabilities. Downloadable for off-line use, local installation or modification.

  Protein Explorer, Advanced:
Choose any molecule, and explore it in Chime. Protein Explorer makes advanced capabilities of Chime easy to use. The Contact Surfaces form produces overviews of noncovalent bonds at interfaces, which can be rendered as solid or transparent surfaces. Cation-pi interactions and salt bridges can be displayed. The Noncovalent Bond Finder makes easy a detailed exploration of hydrogen bonds, hydrophobic interactions, and water bridges. Ensembles of models (as from NMR or morphs) can be played as a movie with custom rendering and coloring. Molecules can be colored to indicate conservation or mutation frequency based on multiple protein sequence alignments (MSA3D). A nonvolatile "expert" preference setting bypasses help for novices.See the Snapshots. See also Protein Explorer for Novices. Downloadable for off-line use, local installation or modification.

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  Protein G Structure Tutorial:
In a frames format, the B1 domain of protein G from Streptococcus is used to highlight several features of protein architecture that are found in many other proteins. In addition, each of the Chime images and the buttons that modify them serve as starting points for making changes in the displays.

  Protein Kinase CKII:
A series of Chime-based tutorials illustrating the structure and function of casein kinase II (CKII), a highly conserved member of the S/T/Y protein kinase family. The three tutorials in the series are designed to be viewed sequentially and address
  1. the alpha subunit monomer (maize)
  2. the beta subunit dimer (human)
  3. the holoenzyme tetramer (human)
Each tutorial consists of a narrative description accompanied by integrated Chime animations that illustrate the major points. The animations, intitated by clicking buttons, can be viewed with minimal viewer interaction, but the user can also manipulate the structures via the Chime pop-up menu. (Note: The stereo mode has been set to cross-eyed rather than default wall-eyed to facilitate viewing in stereo on screen).

  Protein Secondary Structure, versions 1.0, 2.0, 3.0:
Chime presentations of fundamental folding patterns of proteins, the alpha helix and beta sheet. Emphasis is on understanding why polypeptide chains fold in these patterns, and how these secondary structures fit into proteins. Versions 2.0 and 3.0 are self-paced tutorials with textual explanations for each movie button. Version 3.0 features extensive hyperlinked definitions and explanations, enabling viewers to control the depth of the tutorial. Version 1.0 is designed for instructor use in a lecture format, is implemented with movie buttons that are labelled by key words only, and includes brief sections on the eye-catching Green Fluorescent Protein, others. All include brief Chime Help section.

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  Protein Structure Analysis Using Internet Tools: A Tutorial Using Peroxidase:
This resource uses Chime to demonstrate the uses of a selection of online protein databases and resources to look at the structure of peroxidases. Among the databases that are introduced are: The Protein Data Bank, SCOP, CATH, FSSP, SAS, 3D-SEARCH.

  Protein Structures List:
An index page of links to one-page Chime displays of the structures shown in Chapter 4 of Campbell (and many other biochemistry textbooks). The corresponding figure (or page) numbers are shown. Each page illustrates an important structural feature or general principle found in other proteins. The emphasis here is on the overall architecture of proteins rather than specific functions of individual amino acid residues (more on this topic later!). Mastery of the key principles is required for the course.

  Protein Tyrosine Phosphatase PTP1B (at The Online Macromolecular Museum):
The phosphorylation status of a protein can modulate its function, and Protein Tyrosine Kinases (PTKs) and Protein Tyrosine Phosphatases (PTPs) work to regulate protein function in response to a variety of signals, including hormones, mitogens, and growth factors. This Chime-based exhibit focuses on recent structural work on PTP1B, a well studied non-receptor PTP. A homology model of a recently discovered FERM-PTP (Pez) is also discussed.

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  Protein/DNA interactions:
This web resource uses Chime to illustrate one of the final year modules of a biochemistry course covering Protein/DNA interactions. The pages have been written with education in mind, and there is also a "Chime Trainer Page" developed alongside the web pages designed to train students in the use of Chime. The user interface incorporates buttons within frames to create a walkthrough tutorial effect for each of the specific DNA/Protein interactions that are covered.From the initial page the chime resources can be found by navigating through the links to lectures with Chime tutorials, and then scrolling to the bottom of these pages where a button to open the chime tutorial can be found.

  Proteínas: aspectos estructurales básicos:   (Spanish )
This is a basic tutorial on protein structure based on Jmol. It is very simple and starts with amino acids, peptide bond, principles of protein folding and secondary and tertiary structure. There is also a page devoted to domains and super-secondary structures   

  Ras Oncogene Product:
This CHIME enhanced presentation is targeted at advanced undergraduate students taking courses in Biochemistry or Cell Biology. This presentation introduces oncogenes and biological signal transduction before turning to ras as an example of a molecular switch. The two conformations of RAS are displayed using CHIME and the user can easily switch between them. Lastly the structural basis for the two classes of oncogenic ras mutants (i.e. those affecting GTPase activity and those affecting nucleotide affinity) are discussed.

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  RecA Protein (at The Online Macromolecular Museum):
The RecA protein of E. coli is a critical enzyme in DNA recombination, as it catalyzes the pairing of single-stranded DNA with complementary regions of double stranded DNA. In addition to its role in homologous recombination, RecA functions as a coprotease for the LexA protein during the SOS response. This Chime-based exhibit explores the structure-function relationships of this complex enzyme.

  Redox Proteins:
Redox Proteins is an Internet tutorial intended as a computer-based laboratory exercise for undergraduate students in biochemistry. It covers organic redox cofactors, redox enzymes with organic cofactors, cytochromes, iron-sulfur proteins, copper proteins, complexes of redox proteins and multisubunit redox proteins. The tutorial makes use of the Chemscape Chime plug-in and JavaScript. Particular attention has been paid to the design of the user interface so that students which are not so experienced with computers can navigate easily through the tutorial. A form with simple questions is included. Extensive help is available to guide the user.

  Restriction Enzymes: Eco RV:
Eco RV is used to explain the fundamental principles of restriction enzyme action on double-stranded DNA. Domain structure, specific and non-specific binding to DNA, bending of DNA, and catalytic site structure are emphasized. Smooth transitions between views show their relationships clearly. The interface is easy to use for students and novices, but advanced users can modify the images with menus, or enter Chime commands.

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  Retinoid X Receptor, Human:
This presentation is focusing on the basic structure of human retinoid X receptor and the conformational changes upon ligand binding. The presentation starts with the unliganded form of the receptor and ends with the liganded and unliganded forms aligned in one image.

This presentation is in the Protein Explorer (v.1.72 beta) using Chime. It is a prototype of this presentation mode. From any image in the presentation, you can move into Explorer to change the display, color scheme, hide portions and zoom, etc., then return to the presentation.

  Ribosome Tour:
An introductory tour of the ribosome suitable for high school or college general biology classes. Includes the two RNA subunits, numerous proteins, 3 transfer RNAs, and messenger RNA. Based on the first structure for the complete ribosome, reported in May, 2001, by Noller and coworkers. Requires CHIME plug-in. The presentation is actually in Protein Explorer, and therefore makes exploration beyond the defined views easy.

  RNA Silencing Suppression by a Plant Viral Protein: Structural Basis:
This is a Presentation in Protein Explorer, that at the present time relies on the Chime plugin. It explores the structure of plant virus RNA silencing suppressor protein, p19, bound to a small double-stranded silencing RNA, or siRNA. Especially nice is that this presentation is fully integrated into Protein Explorer, thanks to Eric Martz's template, and so you can go to easily explore other structure aspects via the power of Protein Explorer and return to the presentation seamlessly.

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  Rubisco: a first look at the mechanism. An experiment in molecular visualisation.:
'Rubisco: a first look at the mechanism' is an experiment in molecular visualisation using an innovative framing approach to CHIME based tutorials - now also available using Jmol. Exploring the mechanism of 'the world's most abundant enzyme', throws light on why Rubisco is also one of the slowest enzymes (turnover rate of 3 /sec). After consulting the excellent Chime demonstration of the structure of Rubisco and having a look at Schreudr.kin, you begin an interactive Chime tutorial. The tutorial looks in detail at: changes to the substrate RuBP; activation of Rubisco; coordination at the metal site; loop 6 and the N-terminus of neighbouring L chain; changes round the P1 and P2 sites; access to the active site; the contribution of loop 6; access to the active site; the neighbouring L subunit; the reason for isolating the active site? the timing of active site closure; the role of the small subunit S and other issues. A formulation of the mechanism outlined in the publications of I. Andersson et al (e.g.J. Mol. Biol. 259, 160-174) is compared with the formulation published in Cleland et al (Chem. Rev. 98, 549-561). The tutorial, which requires substantial time, was originally written under the auspices of PPS99. Constructive feedback is welcome. The tutorial  works either with Netscape 4 or IE6 and Chime 2.6 SP4. A Jmol version is now available  

  Sickle Cell Anemia: Understanding the Molecular Biology:
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.

  Side-by-Side Amino Acid Viewer:
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.

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  Signal Recognition Particle:
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.

  Signal Recognition Particle Core (at The Online Macromolecular Museum):
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.

  Small Molecule 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.

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  Structural Alignment Program for Proteins:
STRAP is an interactive editor for multiple sequence alignments of proteins. Several tutorials and wizards on the following topics are integrated in STRAP:
  1. mapping of mutations and polymorphisms onto three-dimensional protein structures
  2. multiple structure alignments
  3. BLAST searches
  4. evolutionary dendrograms
  5. multiple sequence alignments of sequences with little similarity
These tutorials are the basis for training courses which are offered for students of biophysics, biochemistry and biology at the Humboldt University Berlin

  Structural Biochemistry of Blood Coagulation:
The structures of many blood coagulation factors have been determined experimentally by X-ray crystallography or by NMR spectroscopy. These pages illustrate structural features of these proteins using Chime. Included are tissue factor (factor III); a tissue factor + factor VII complex; von Willebrand factor; tissue factor pathway inhibitor; protein C; a portion of factor IX containing several gamma-carboxy-glutamate residues; thrombin (factor II, complexed with hirudin, a leech anticoagulant); factor XIII; a fibrin fragment.

  Structures for Molecular Biology:
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.

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  Student Webpapers: The Structure-Function Relationships for the Enzymes in the Glycolytic and Lactate Fermentation Pathways.:
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:

  SV40 capsid structure and assembly.:
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.)  

  The 20 common amino acids:
Each amino acid is displayed (with hydrogens) in Chime in a table including names, structural formulae of both the ionized and nonionized forms, isoelectric points and pK values.

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  The E. coli trp Repressor Chime Movie:
This Chime movie illustrates the structural differences between crystal structures of the inactive apo form (3WRP) and liganded active form (1TRO) of trp repressor, a DNA binding protein from E. coli. Both structures are superimposed in a single PDB file which is downloaded to the left frame. Apo vs. holo forms are selected by toggling push buttons, and the trp operator DNA can also be toggled on and off. The site was designed to make it possible to easily compare these structures, and to illustrate one of few examples where the structural basis for ligand-activation of a DNA-binding protein has been clearly elucidated using crystal structure analysis.

  The Glycolytic Cycle:
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.

  The Guided Tours of Metalloproteins (now with Jmol or Chime):
Take guided tours of the metal ions sites found in metalloproteins and model complexes that have been synthesized to mimic the structure or function of these sites. The tours require a browser working with JAVA (a free download for PC or Linux computers, standard for Macintosh computers). The tours make use of free Jmol software that is automatically provided by the browser on your computer. An older version of the Tours is also available for Windows computers equipped with the Chime plugin, available as a free download.

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  The Large Ribosomal Subunit: a structure/function tutorial:
By this point, the ribosome should be a familiar object in your biochemistry/biology education because all life as we know it requires a ribosome to construct proteins. The peptide bond formation it catalyzes is rather simple; however, the complete molecule must also read mRNA codons, and bind 3 tRNA molecules. This accounts, in part, for the large size of the molecule. Unfortunately, much of the mechanism remains a mystery. In a series of papers published in 2000, researchers have determined the structure of the large subunit to a great degree of accuracy, and have proposed specific residues which catalyze the peptide bond formation in large subunit. In this tutorial, we will examine the large subunit, and in doing so, will address three related questions. Which of the components of the large subunit comprise the active site, where is that site located, and how does it work? This tutorial uses the Chime plugin to visualize the three dimensional structure of the ribosome and to animate the mechanism of peptide formation.

  The Lycoming College Macromolecular Modeling and Bioinformatics Page:
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.

  The Rational Basis of Drug Design:
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).

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  The Zinc Finger: A Protein Domain that Binds Specific DNA Sequences:
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.

  Thermal motion of alpha helix:
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).

  tRNA Tour:
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".  
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  U1A Spliceosomal Protein (at The Online Macromolecular Museum):
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.  

  Viral Antigens (at The Online Macromolecular Museum):
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).  

  Water Simulation:
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.
Now also in Jmol version, English and Spanish (look below).

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  Water Simulation - using Jmol:
A theoretical simulation (done with MDL Sculpt) of 10 water molecules assembling into a compact, hydrogen-bonded network. Available as a Jmol animated model. Ten questions are provided for students about the final hydrogen-bonded droplet.

  Web-Based Chemical Investigations:
Interactive tutorials in general and organic chemistry and biochemistry using Chime. Modules includeBiochemistry modules are listed individually under Bragin in the author index. These tutorials use a discovery-based approach to learning concepts.  

  XdomView: A Chime-based Graphical Tool for Protein Domain and Exon Position Visualization:

Enlarged image

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.

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.

  
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  Zinc Binuclear Clusters:
Zinc binuclear clusters are motifs found in transcriptional regulatory proteins in fungi. An early zinc binuclear cluster was originally thought to be similar to previously described zinc fingers, with four cysteines forming a tetrahedral zinc binding site. Subsequent structural studies strated that the zinc binuclear cluster consists of 6 cysteine residues that are bound to two zinc atoms. This documentary includes text, images, sequence and structural data and molecular visualizations to describe representative members of this family. It is presented in the BioEditor software package.
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160 total titles.
Visitor-Maintained Index programming by Trevor D. Kramer.