Israeli National Node - Open Day 2000
Protein Explorer and Chime Resources
from Eric Martz, University of Massachusetts, Amherst MA USA
for Workshops at Israeli National Node,
Weizmann Institute of Science, June 2000
Most of the software below is open-source freeware, and can be used
directly from the web, or downloaded for off-line use.
Most was supported by the National Science Foundation.
Free software for visual exploration of macromolecular structure.
Version 1.47 is much easier for novices to use than RasMol, and
more powerful. Yet it understands all RasMol commands.
The first view of each molecule is maximally informative, described
and interpreted by the FirstView page. QuickViews provides simple,
logically organized yet powerful menus (find noncovalent bonds between
ligand and protein in one click). Seq3D displays the amino acid
sequence -- clicking on a residue or range identifies it in the 3D
structure. Advanced Explorer generates rolling probe surfaces (can be
colored by MEP, MLP), and can play ensembles of models (NMR) as movies,
and colors a 3D structure according to a multiple protein sequence
Class websites can include hyperlinks to Protein Explorer which
prespecify molecule(s). Adopted by the Protein Data Bank as a 3D
structure viewer. Authored by Eric Martz, using MDL Information Systems'
Chemscape Chime freeware.
A search interface for the Protein Data Bank designed for students,
educators, and occasional users. Jargon is avoided or explained.
Detailed instructions for downloading PDB files so you can open them
in RasMol or Protein Explorer, Tabular summary is easy to scan. Disallows
syntax which gives false misses. Automatic synonym searching ("hemoglobin"
finds "haemoglobin"). Mirrored around the globe. Authored by Eric
Martz and Jaime Prilusky in 1998; upgraded by Jaime Prilusky in 1999-2000 to work
World Index of BioMolecular Resources in Chime.
Newly a "Visitor-Maintained Index": additions or changes supplied
by visitors via web form are immediately alphabetized into the
subject and author indices. Visitors can enter hyperlinks,
describe the resource, and provide subject or molecule name
Two categories: Ready-To-Use Resources, and How To
Create New Resources. Version two, now in preparation, when
released will allow visitors to rate and comment upon indexed
resources. Visitor-Maintained Index program authored by Trevor
Kramer and Eric Martz.
Assembly of the SV-40 capsid from 360 copies of the VP1 protein monomer is
explained as a presentation within Protein Explorer. Any image in
the presentation can be explored at will with the full
capabilities of Protein Explorer. Another presentation is also
here on the bacterial cell division protein FtsZ. These are
prototypes; the template for creating new Presentations in
Protein Explorer (PIPE) is still under development. Presentations
by Stefan Welte, Gabe McCool, and Eric Martz.
Displays morphs of protein conformational changes as "movies". Examples
include the binding of calcium to EF hands, and the resulting conformational
change in recoverin (a calcium-activated myristoyl switch). Instructions
are provided for creating your own morphs using linear interpolation or
"chemically plausible" intermediates calculated with software by
Werner Krebs and Mark Gerstein (Yale) or Gerard Kleywegt (Uppsala).
The resulting morphs (in NMR PDB format) can be most easily played as movies
in Protein Explorer.
DRuMS Standard Color Schemes for Macromolecules.
A proposed standard set of color schemes for proteins and
polynucleotides authored by Tim Driscoll, Frieda Reichsman, Eric
Martz, and Roger Sayle. Freely available for educational or
commercial use. Adopted in Protein Explorer, and Biochemistry in
3D (see below). Website provides rationales, demonstrates color schemes
on variety of molecules, and offers for download Chime scripts
which apply the color schemes to any molecule.
NonCovalent Bond Finder.
An automated tool in Chime that finds the closest contacts
between any two sets of atoms. Pressing the [Find] button
repeatedly steps out in 0.1 Angstrom increments. Fill out the
residues to which atoms belong in a single click. By Eric Martz,
released in 1998.
Biochemistry in 3D.
A new, superb, state of the art Chime website with interactive tutorials
on protein architecture (from amino acids through peptides, secondary, tertiary
and quaternary structure), trimeric G proteins, bacteriorhodopsin, myoglobin
and hemoglobin. Written by Tim Driscoll, Freida Reichsmann and others.
Additional tutorials on protein structure, DNA and DNA-binding
proteins authored by Frieda Reichsman are at the second site below.