Advanced Protein Explorer Workshop
Center for Molecular Modeling, NIH
January 5, 2001 - Eric Martz (firstname.lastname@example.org)
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
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 www.umass.edu/molvis/workshop/w2nih01.htm.
To start Protein Explorer, in Netscape, go to
www.proteinexplorer.org (the "www" is optional).
Possible topics for the workshop include:
- Overview or Protein Explorer's QuickViews menus and Seq3D
for selection, display, and coloring.
- Sequence irregularities (insertions and non-physical gaps, 1igt;
physical gaps, 2ace; microheterogeneity, 1cbn).
- Protein Explorer's preferences: expert mode.
- 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.
- 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.
- Using CaPTURE to determine energetically significant
cation-pi interactions. (See the Tutorial in Advanced Explorer's
- MSA3D: Coloring a molecule according to a multiple protein
- Obtaining a multiple protein sequence alignment at
the Biology Workbench. (See the Tutorial in Advanced Explorer's MSA3D.)
- Searching for structurally similar proteins, without
reference to sequence: CE (Combinatorial Extension, Shindyalov &
Bourne), Vector Alignment Search Tool (US National Center for
- Surfaces colored by electrostatic potential or
molecular lipophilicity potential. (See Advanced Explorer, Surfaces)
- Probable quaternary structures (virus capsids, etc.)
See the link to EBI at the FrontDoor. Also getting single chains,
see ExPDB at molvisindex.org (under sources of PDB files).
- 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.
- Morphing: making movies of protein conformational changes.
www.umass.edu/microbio/chime/morpher for demonstrations and methods.
- Exploring Crystal Contacts. An example is at
and see the alpha version of a crystal contact server by Gert Vriend
at www.cmbi.kun.nl:1100/WIWWWI (under Symmetry).
- Presentations in Protein Explorer. See
www.umass.edu/microbio/chime/pipe and methods including an alpha-version
of a script recorder downloadable at
and scripts for Chime.