Macromolecular 3D visualization and analysis in Protein Explorer

Eric Martz, Professor, University of Massachusetts, Amherst MA US

Protein Explorer 2.0 (PE, www.proteinexplorer.org) offers powerful 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, salt bridges, animate conformational changes, and color a 3D protein by conservation/mutation from a multiple protein sequence alignment. PE is freeware for Windows or Macintosh.