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Macromolecular Geometry
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.[ Citation info | NucProt | Packing-Eff Online! | Old front page ]
Downloadable software Documentation
- 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, available in a 'basic version', which includes accessible surface and volume among other calculations, and an advanced version, which does only volume and surface calculations and has extra parameter choices. (This was set up by Susan Chacko at the NIH.)
- PGC: The Protein Geometry Calculator
- 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)
Other Resources
- 3DHMM and Structural Alignment Code
- Picture gallery (at bioinfo.mbb.yale.edu)
- A script for selecting parameter sets
- Related software packages at the Center for Structural Biology at Yale
Copyright 1995-2003, M. Gerstein and others
Email: Mark.Gerstein@yale.edu
This page created by Julian Graham
Last modified by Neil Voss on Feb 24, 2006
