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 over 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.
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== Resources and Downloadable Software ==
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== Resources and Downloadable Software for Packing ==
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*[http://tace.molmovdb.org/tacehome.html TACE] calculates pseudo-torsion angle changes in backbone structures given a pair of conformations.
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*[http://geometry.molmovdb.org/nucprot/ NucProt Site] analyzes voronoi volume and packing of RNA structures.
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*[http://geometry.molmovdb.org/nucprot/ NucProt Site] analyzes Voronoi volume and packing of RNA structures.
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*[http://www.molmovdb.org/cgi-bin/voronoi.cgi Packing-Eff Online] voronoi method for packing efficiency.
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*[http://www.molmovdb.org/cgi-bin/voronoi.cgi Packing-Eff Online] Voronoi method for packing efficiency.
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*[http://3vee.molmovdb.org/ 3V] volume related calculations.
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*[http://3vee.molmovdb.org/ 3V] Calculates cavities & channels in macromolecular structures
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*[http://geometry.molmovdb.org/3dhmm/ 3D HMM] compares protein structures.
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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]
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*Geometry library with sample programs
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*Geometry library with sample programs ([http://geometry.molmovdb.org/files/libproteingeometry/README.html README])
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**[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])
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**[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/protgeom21_w32.zip 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)
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*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)
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== Other Resources and Downloadable Software ==
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*[http://tace.molmovdb.org/tacehome.html TACE] calculates pseudo-torsion angle changes in backbone structures given a pair of conformations.
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*[http://geometry.molmovdb.org/3dhmm/ 3D HMM] compares protein structures.
*PGC: The Protein Geometry Calculator
*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)
**[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)

Revision as of 00:59, 2 April 2016

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

Other Resources and Downloadable Software

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

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