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.



*Source Code

A library of C source code is available. It contains programs for calculating volumes (using the Voronoi method), surfaces contacts, and other parameters relevant to the protein surface. It also contains code for doing a least-squares fit of two structures and for calculating geometrical parameters such as helix axes. Also, there is: Check out "beta" of version 2.0 of source code release.

*Standard volumes

A file giving statistics on the volumes for buried core atoms in a database of 119 structures. These reference atomic volumes can be compared to the volumes calculated with the volume program (above) to see how well-packed a given atom is.

*Picture Gallery

28 January 2003 /
1 May 1997 /