Advanced Protein Explorer Workshop
Weizmann Institute of Science

June 25, 2000 - Eric Martz (emartz@microbio.umass.edu)

The agenda for this workshop will be informal, and will adapt to the interests of the participants. Collaborations are invited that use Protein Explorer to display information about macromolecular structure, particularly information which may be the result of your research.

Possible topics for the workshop include:

  1. Overview or Protein Explorer's QuickViews menus and Seq3D for selection, display, and coloring.

  2. Sequence irregularities (insertions and non-physical gaps, 1igt; physical gaps, 2ace; microheterogeneity, 1cbn).

  3. Protein Explorer's preferences: expert mode.

  4. Contact Surfaces for an overview of the noncovalent bonds between any two moieties. For a start, use QuickViews' DISPLAY menu, selecting Contacts. Then, under Advanced Explorer's Contact Surfaces page are many more options.

  5. The NonCovalent Bond Finder: a press of the [Find] button displays the atoms closest to any moiety. Additional clicks on [Find] step out in 0.1 Angstrom shells. Clicking on a found atom displays the whole residue to which it belongs. Distances from putatively bonded atoms can be displayed. To keep the image simple, hydrogen bonds and hydrophobic interactions can be dealt with in separate scans.

  6. MSA3D: Coloring a molecule according to a multiple protein sequence alignment.

  7. Obtaining a multiple protein sequence alignment at the Biology Workbench.

  8. Searching for structurally similar proteins, without reference to sequence: CE (Combinatorial Extension, Shindyalov & Bourne), Vector Alignment Search Tool (US National Center for Biotechnology Information).

  9. Surfaces colored by electrostatic potential or molecular lipophilicity potential.

  10. Structural alignment of two or more molecules. The CE site will align any two protein chains quickly and easily (but hetero atoms are discarded). Swiss PDB Viewer 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. http://www.expasy.ch/spdbv/mainpage.html.

  11. Morphing: making movies of protein conformational changes.

  12. Authoring Chime resources with javascript, executeChimescript(), and scripts for Chime.
To find this page on the web, go to the RasMol Classic Main Page (www.umass.edu/microbio/rasmol) and click on Education, then Software training, then look under the list of workshops.