Macromolecular Geometry

From Info

Revision as of 22:41, 25 June 2008

We are interested in the calculation of geometrical quantities associated with macromolecular structures and their motions. These include volumes, surfaces, axes, angles, and distances. Volumes and other quantities related to packing are of particular interest. For instance, one goal is to characterize the special type of atom-to-atom packing that occurs at interfaces, such as those between a protein and water. This analysis is motivated by the work on protein packing begun by Fred Richards a quarter century ago.

Downloadable Software

• NucProt Site
• Packing-Eff Online
• Parameter Sets for Geometry Programs
• Geometry library with sample programs
  • libproteingeometry-2.3.1.tgz (full distribution v2.3.1) (README)
  • Windows binaries, src-diff (provided by Donald Gaffney at U Vermont)
• A server for calculating geometric quantities, which includes accessible surface and volume among other calculations. (This was set up by Susan Chacko at the NIH)
• PGC: The Protein Geometry Calculator
  • pgc-1.0b.tar.gz (http://geometry.molmovdb.org/files/pgc/README.txt README)
  • Screenshots
    • Some simple pgc expressions
    • Voronoi volumes for the residues a structure

Documentation

• Selected talks (at bioinfo.mbb.yale.edu/lectures)

"Determination of a screw axis for describing protein motions from a rotation matrix and a translation vector" (1997) (html) "Protein Volume and Surface Area" (1996) (html)

• Older version of "Protein Volume and Surface Area" (1995) (html)

"Methods for the Generation and Analysis of Protein Simulations" (1995) (compressed postscript) (rtf)