Macromolecular Geometry

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*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])
**libproteingeometry-2.3.1.tgz (full distribution v2.3.1) ([http://geometry.molmovdb.org/files/libproteingeometry/README.html README])
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**Windows binaries, src-diff (provided by Donald Gaffney at U Vermont)
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**Windows binaries, [http://geometry.molmovdb.org/files/libproteingeometry-2.1.diff src-diff] (provided by Donald Gaffney at U Vermont)
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*A [http://molbio.info.nih.gov/structbio/basic.html 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.)

Revision as of 21:55, 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, 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.)
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