Macromolecular Geometry
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*[http://geometry.molmovdb.org/files/libproteingeometry/data/ Parameter Sets for Geometry Programs] | *[http://geometry.molmovdb.org/files/libproteingeometry/data/ Parameter Sets for Geometry Programs] | ||
*Geometry library with sample programs | *Geometry library with sample programs | ||
| - | **libproteingeometry-2.3.1.tgz (full distribution v2.3.1) ([http://geometry.molmovdb.org/files/libproteingeometry/README.html README]) | + | **[http://geometry.molmovdb.org/files/libproteingeometry-2.3.1.tgz libproteingeometry-2.3.1.tgz] (full distribution v2.3.1) ([http://geometry.molmovdb.org/files/libproteingeometry/README.html README]) |
| - | **Windows binaries, [http://geometry.molmovdb.org/files/libproteingeometry-2.1.diff src-diff] (provided by Donald Gaffney at U Vermont) | + | **[http://geometry.molmovdb.org/files/protgeom21_w32.zip Windows binaries], [http://geometry.molmovdb.org/files/libproteingeometry-2.1.diff src-diff] (provided by Donald Gaffney at U Vermont) |
| - | *A [http://molbio.info.nih.gov/structbio/basic.html server] for calculating geometric quantities, | + | *A [http://molbio.info.nih.gov/structbio/basic.html 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 | ||
| + | **[http://geometry.molmovdb.org/files/pgc/pgc-1.0b.tar.gz pgc-1.0b.tar.gz] (http://geometry.molmovdb.org/files/pgc/README.txt README) | ||
| + | **Screenshots | ||
| + | **[http://geometry.molmovdb.org/images/pgc/pgc-shot-01.png Some simple pgc expressions] | ||
| + | **[http://geometry.molmovdb.org/images/pgc/pgc-shot-02.png Voronoi volumes for the residues a structure] | ||
| + | |||
| + | == Documentation == | ||
Revision as of 22:37, 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
