Protein Explorer/NIH-CMM

Protein Explorer and Chime Resources
Guide for the Center for Molecular Modeling, NIH, January 2001
from Eric Martz, University of Massachusetts, Amherst MA USA (emartz@microbio.umass.edu)

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. This guide is available on-line: www.umass.edu/molvis/workshop/nihcmm01.htm

Protein Explorer (PE) version 2.0 enables visualization of macromolecular 3D structure with exceptional ease of use. Visual analysis of proteins, nucleic acids, and ligand interactions can be done largely from menus, buttons, and forms, with context-sensitive help and color keys displayed automatically. PE employs the Chime plugin that is derived from RasMol, and PE understands all RasMol commands. However PE enables visual analysis to considerable depth without learning a single RasMol-style command, and it is much more powerful than RasMol. PE enables easy selection of portions of a molecule, to apply different rendering or coloring schemes, and to hide selected moieties. In addition it has one-click routines to map sequence to structure, show contact surfaces (overview of noncovalent bonds to any moiety), solvent-accessible surfaces, cation-pi interactions, and salt bridges. Advanced routines simplify finding noncovalent bonds, and coloring a protein by conservation/mutation from a multiple protein sequence alignment. Websites can include hyperlinks to Protein Explorer that 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. PE is freeware for Windows or Macintosh. proteinexplorer.org
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 that 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 the OCA browser. pdblite.org
World Index of Molecular Visualization Resources. "Visitor-Maintained": 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. Categories include Biochemistry, Organic Chemistry, Inorganic Chemistry and Crystals, How To Create New Chime Resources, Sources of Molecules (PDB files), K12 Resources, Swiss-PDB Viewer Resources, Molecular Galleries, EMail Lists, Non-English Resources, Free and Commercial Software. Visitor-Maintained Indices program authored by Trevor Kramer and Eric Martz. molvisindex.org
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
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. www.umass.edu/microbio/chime/find-ncb (also available within Protein Explorer)
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, and restriction endonucleases. 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
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 that apply the color schemes to any molecule. www.umass.edu/molvis/drums
Presentations in Protein Explorer (under development). Support for tutorials and molecular structure presentations within Protein Explorer is under construction. Collaborations are planned for visualization of protein structure research and bioinformatics results. Parties interested in such collaborations are invited to contact emartz@microbio.umass.edu. The tutorials will appear similar to most existing Chime tutorials (see the World Index above) with buttons producing a series of author-prepared images in Chime. However, from any image in the tutorial, one can move seamlessly into Protein Explorer, then back into the tutorial. Prototype demonstrations: SV-40 Capsid assembly from 360 copies of the VP1 protein monomer, by Stefan Welte. Bacterial Cell-Division protein FtsZ by Gabe McCool. www.umass.edu/microbio/chime/pipe
High-Detail Physical Molecular Models. 3D Molecular Designs manufactures high-detail molecular models from atomic coordinate files. A computer model is converted to an engineering format (stereolithography), which instructs a selective laser sintering machine to create a nylon model (see figure at www.umass.edu/microbio/chime/beta/molcad/1hsa.jpg). www.3dmoleculardesigns.com

Workshops
Protein Explorer for Novices: www.umass.edu/molvis/workshop/w1nih01.htm
Advanced Protein Explorer: www.umass.edu/molvis/workshop/w2nih01.htm