Protein Explorer/INN-WIS

Israeli National Node - Open Day 2000

INN Protein Structure Server. Software and databases for molecular visualization. inn-prot.weizmann.ac.il

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.

Protein Explorer. 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 alignment (MSA3D). 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. inn-prot.weizmann.ac.il/martz/protexpl
(or www.umass.edu/microbio/chime/explorer)
PDB Lite. 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 with OCA. bioinfo.weizmann.ac.il:8500/oca-bin/pdblite
www.umass.edu/microbio/rasmol/pdblite.htm
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 cross-indexing terms. 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. www.umass.edu/microbio/rasmol/tutbymol.htm
SV40 Capsid. 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. www.umass.edu/microbio/chime/pipe
Protein Morpher. 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. www.umass.edu/microbio/chime/morpher
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. www.umass.edu/molvis/drums
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. inn-prot.weizmann.ac.il/martz/find-ncb
(or www.umass.edu/microbio/chime/find-ncb)
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. www.worthpublishers.com/lehninger3d www.umass.edu/molvis/freichsman