Rationale: In this day of exploding bioinformatics information from genomics and proteomics, it is ever more important to be conversant with macromolecular three-dimensional structure, and how it relates to protein and nucleic acid function and rational drug design. This workshop will enable participants to find published molecular structure data, and visualize and interpret 3D molecular structure. Participants will be enabled to incorporate computer visualization of protein, DNA, and RNA into their teaching and research.

Software: The central tool for this workshop is Protein Explorer (www.proteinexplorer.org). Protein Explorer is free, operates on Windows or Macintosh (also linux), and is much easier to use, yet much more powerful than RasMol. Protein Explorer has been adopted for visualization of macromolecular 3D structure by the Protein Data Bank (www.pdb.org).

Level & Pace: This workshop is designed for educators and biological scientists familiar with basic biochemistry, but with no previous molecular visualization software experience. It progresses rapidly to powerful tools that will be of interest to researchers, including specialists in protein structure and bioinformatics. Experienced participants are encouraged to work at their own speed, ahead of the group -- there is plenty of power in Protein Explorer to discover!

Hyperlinks: To click the hyperlinks below, go to this document on the web,

Tuesday April 24. Basics. How to use Protein Explorer to visualize structural features of proteins and nucleic acids. Observations may be recorded on a form provided.

FirstView
1. Use of the mouse to rotate the molecule; clicking to identify atoms.
2. Identifying and becoming familiar with the computer representations for chains, backbones, disulfide bonds, solvent, and ligands.

   QuickViews

3. Selecting, emphasizing, and hiding portions of the molecule.
4. Zooming, centering.
5. Backbone, trace, cartoon, stick, ball and stick, spacefill to van der Waals radii.
6. Coloring by element (Corey, Pauling, Koltun color scheme).
7. Coloring cartoons by secondary structure.
8. Identifying the amino and carboxy termini (5', 3' ends): N->C Rainbow (Group) color scheme.
9. Interpreting the distribution of hydrophobic, polar, and charged residues (Polarity color schemes).
   • Potassium channel: 1bl8. Trp prefers lipid-water interface.
   • Gramicidin in a lipid bilayer: bilagram.pdb
10. Coloring to distinguish A, T, G, C, U. How to distinguish DNA from RNA.
11. Coloring by disorder: temperature factor coloring.

    Sequences

12. Protein Explorer's Sequence display.
    • Insertions and non-physical gaps: 1igt.
    • Physical gaps: 2ace, 1fod.
    • Microheterogeneity: 1cbn.
13. Protein Explorer's clickable Seq3D
    • Sequence to 3D structure mapping.
    • Finding all instances of one amino acid (e.g. cysteine).
    • Selecting and coloring an arbitrary range of residues.

14. Free time to review and explore.

Wednesday April 25: Finding molecules of interest. Exploring and interpreting their structures. Animations. Observations may be recorded on a form provided.

15. Overview of origin, nature, and limitations of molecular structure data (X-ray crystallography, nuclear magnetic resonance).
    • www.rcsb.org/pdb/experimental_methods.html
16. The Protein Data Bank
    • www.rcsb.org
17. Finding molecules of interest.
    • PDB Lite: www.pdblite.org
    • RCSB's SearchFields www.pdb.org
    • Prilusky's OCA bioinfo.weizmann.ac.il:8500
18. Getting information about your molecule.
    • Protein Explorer's Molecule Information Window:
      • PDB File Header
      • Probable Quaternary Structures
      • Crystal Contacts
      • Model Quality (& examples of errors in published PDB files)
      • RCSB's Structure Explorer.
    • NCBI Entrez, PubMed www.ncbi.nlm.nih.gov
19. Animations.
    • Multiple-model NMR PDB files: simulation of thermal motion.
    • Morphs of conformational changes.

20. Free time to explore participant's molecules.

Thursday April 26: Contact surfaces reveal noncovalent bonds. Cation-pi interactions and salt bridges. Coloring a 3D protein by conservation/mutation from a multiple protein sequence alignment (MSA3D).

21. Contact surfaces. Example: Gal4 contacting DNA (1d66), showing:
    • Nonspecific charge interactions at DNA backbone phosphates,
    • Sequence specific recognition DNA bases by zinc finger domain of protein,
    • Hydrophobic protein-protein interaction.
22. Visualizing cation-pi interactions and salt bridges.
23. Preferences in Protein Explorer.

24. Demonstration of Protein Explorer's MSA3D.
25. Building a multiple protein sequence alignment.
    • Biology Workbench workbench.sdsc.edu
26. Locating regions of conservation or mutation with Protein Explorer's MSA3D.

27. Free time to review and apply new methods to your molecule.

Friday April 27: Optional day (attendence not required) for individual work, or topics chosen by those attending. Use what you've learned. Possible new topics:

28. Hydrogen bonds.
29. The Noncovalent Bond Finder.
30. Introduction to using the RasMol/Chime Command Language.
    • Command aliases.

31. Building a web page with hyperlinks to Protein Explorer that prespecify molecules for your teaching or research.
32. Ready-to-use tutorials in Chime for teaching
    • World Index of Chime Resources www.umass.edu/microbio/rasmol/tutbymol.htm
    • Presentations in Protein Explorer www.umass.edu/microbio/chime/pipe
33. Rolling probe surfaces and molecular electrostatic potential coloring.

34. Searching by structure without reference to sequence:
    • Shindyalov & Bourne's Combinatorial Extension cl.sdsc.edu/ce.html
    • NCBI's Vector Alignment Search Tool (VAST) www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml
35. Aligning two or more chains or molecules, and how to view the alignment.
    • The CE site cl.sdsc.edu/ce.html will align any two protein chains quickly and easily (but hetero atoms are discarded).
    • Swiss PDB Viewer www.expasy.ch/spdbv/mainpage.html can align anything (one or more than one chains), selecting any subset of atoms for the alignment (other atoms following), and retaining hetero atoms. The results can be saved as a PDB file. It will need manual editing to separate models with MODEL [N] and ENDMDL records so that Protein Explorer can distinguish the models.
36. Modeling: mutation, homology modeling, crystallographic contacts.
    • Swiss PDB Viewer www.expasy.ch/spdbv/mainpage.html is free and powerful.
37. Building Chime presentation websites.
    • A well tested and debugged template (but will soon be obsolete) www.umass.edu/microbio/chime/prsswc/template.htm
    • Presentations in Protein Explorer (not yet available for general use) www.umass.edu/microbio/chime/pipe

38. Keep in touch!
    • RasMol/Molecular Visualization Freeware/Education email list: www.umass.edu/microbio/rasmol/raslist.htm
    • PDB email discussion: www.rcsb.org/pdb/forum.html
    • Yours truly: emartz@microbio.umass.edu (But please direct questions about RasMol or Chime or Protein Explorer to the RasMol list, first item above.)

39. Free time for individual work.

Collaborations are invited that use Protein Explorer to display information about macromolecular structure, particularly information which may be the result of your research.