Advanced Protein Explorer Workshop
Center for Molecular Modeling, NIH

January 5, 2001 - Eric Martz (

Announcement: This hands-on computer workshop is designed for people having previous experience with macromolecular visualization in any of the many software packages available. It will focus on the capabilities of Protein Explorer and Chemscape Chime, targeting interests expressed by the participants. Topics may include how to use an automated interface for detailed exploration of noncovalent bonds (the Noncovalent Bond Finder); finding energetically significant cation-pi interactions; generating overviews of noncovalent interactions using "contact surface" displays; how to animate functional conformational changes or movements, such as the binding of calcium to an EF-hand; searching for proteins with similar structures (regardless of sequence) and viewing the resulting structure alignments. We may also create multiple protein sequence alignments and color 3D proteins by conservation and mutation frequency. (If you already have some multiple protein sequence alignments, bring them in FASTA/PIR format.) Methods for presenting research results in Protein Explorer, and for controlling Chime with javascript can also be discussed.

Agenda: 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. This page is on the web at

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. Using CaPTURE to determine energetically significant cation-pi interactions. (See the Tutorial in Advanced Explorer's Cation-Pi section.)

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

  8. Obtaining a multiple protein sequence alignment at the Biology Workbench. (See the Tutorial in Advanced Explorer's MSA3D.)

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

  10. Surfaces colored by electrostatic potential or molecular lipophilicity potential. (See Advanced Explorer, Surfaces)

  11. Probable quaternary structures (virus capsids, etc.) See the link to EBI at the FrontDoor. Also getting single chains, see ExPDB at (under sources of PDB files).

  12. 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.

  13. Morphing: making movies of protein conformational changes. for demonstrations and methods.

  14. Exploring Crystal Contacts. An example is at and see the alpha version of a crystal contact server by Gert Vriend at (under Symmetry).

  15. Presentations in Protein Explorer. See and methods including an alpha-version of a script recorder downloadable at

  16. Authoring Chime resources with javascript, executeChimescript(), and scripts for Chime.