World Index of BioMolecular Visualization Resources
Biochemical Structure Tutorials
World Index of BioMolecular Visualization Resources
Biochemical Structure Tutorials
Titles Subjects Authors: Detailed Compact HOME
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.
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.
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.
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.
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.
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.
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.
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.
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).
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.
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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Covers Computation and
Visualization of Electrostatic Potential in PMV.
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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
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.
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.
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.
| 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 |
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.