Macromolecular Geometry
From Info
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 over a quarter century ago.
Contents |
Resources and Downloadable Software for Packing
- NucProt Site analyzes Voronoi volume and packing of RNA structures.
- Packing-Eff Online Voronoi method for packing efficiency.
- 3V Calculates cavities & channels in macromolecular structures
- Parameter Sets for Geometry Programs
- Geometry library with sample programs, includes volume calculation software (README)
- libproteingeometry-2.3.1.tgz (full distribution v2.3.1)
- Windows binaries, src-diff (provided by Donald Gaffney at U Vermont)
Other Resources and Downloadable Software
- TACE calculates pseudo-torsion angle changes in backbone structures given a pair of conformations.
- 3D HMM compares protein structures.
- PGC: The Protein Geometry Calculator
Documentation (fairly old)
- Lecture in course (http://gersteinlab.org/courses/452) describing voronoi volumes.
- Papers on Volumes
- Old
- "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 Stuff
- Picture gallery (at bioinfo.mbb.yale.edu)
- A script for selecting parameter sets
- Related software packages at the Center for Structural Biology at Yale
- OS: Occluded surface and atomic packing
- VOLUME: Voronoi volumes software by F. M. Richards
