# Macromolecular Geometry

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- | 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. | + | 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. |

== Resources and Downloadable Software == | == Resources and Downloadable Software == |

## Revision as of 09:05, 23 March 2011

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.

## Resources and Downloadable Software

- NucProt Site analyzes voronoi volume and packing of RNA structures.
- Packing-Eff Online voronoi method for packing efficiency.
- 3V volume related calculations.
- 3D HMM compares protein structures.
- 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

## 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)

## Other Resources

- 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
- OS: Occluded surface and atomic packing
- VOLUME: Voronoi volumes software by F. M. Richards