Macromolecular Geometry

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(Other Resources and Downloadable Software)
 
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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.
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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.
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== Resources and Downloadable Software ==
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== Resources and Downloadable Software for Packing ==
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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://geometry.molmovdb.org/nucprot/ NucProt Site] analyzes Voronoi volume and packing of RNA structures.
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*[http://geometry.molmovdb.org/3v/ 3V] volume related calculations.
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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://geometry.molmovdb.org/3dhmm/ 3D HMM] for structure comparison.
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*[http://3vee.molmovdb.org/ 3V] Calculates cavities & channels in macromolecular structures
*[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, includes volume calculation software ([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://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)
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***[http://geometry.molmovdb.org/images/pgc/pgc-shot-02.png Voronoi volumes for the residues a structure]
***[http://geometry.molmovdb.org/images/pgc/pgc-shot-02.png Voronoi volumes for the residues a structure]
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== Documentation ==
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== Documentation (fairly old) ==
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*Selected talks (at [http://bioinfo.mbb.yale.edu/lectures/ bioinfo.mbb.yale.edu/lectures])
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* [http://www.gersteinlab.org/courses/452/09-spring/pdf/structure2.pdf Lecture] in course (http://gersteinlab.org/courses/452) describing voronoi volumes.
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*"Determination of a screw axis for describing protein motions from a rotation matrix and a translation vector" (1997) ([http://bioinfo.mbb.yale.edu/geometry/screw-axis/ html])
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* [http://papers.gersteinlab.org/subject/volumes/index.html Papers on Volumes]
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*"Protein Volume and Surface Area" (1996) ([http://bioinfo.mbb.yale.edu/hyper/mbg/SurfVolTalk/new96/svtalk.html html])
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* Old
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*Older version of "Protein Volume and Surface Area" (1995) ([http://bioinfo.mbb.yale.edu/hyper/mbg/SurfVolTalk/svtalk.html html])
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**"Determination of a screw axis for describing protein motions from a rotation matrix and a translation vector" (1997) ([http://bioinfo.mbb.yale.edu/geometry/screw-axis/ html])
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*"Methods for the Generation and Analysis of Protein Simulations" (1995) ([http://bioinfo.mbb.yale.edu/hyper/mbg/SurfaceVolumes/sim-talk/sim-talk.ps.Z compressed postscript]) ([http://bioinfo.mbb.yale.edu/hyper/mbg/SurfaceVolumes/sim-talk/sim-talk.rtf rtf])
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**"Protein Volume and Surface Area" (1996) ([http://bioinfo.mbb.yale.edu/hyper/mbg/SurfVolTalk/new96/svtalk.html html])
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**Older version of "Protein Volume and Surface Area" (1995) ([http://bioinfo.mbb.yale.edu/hyper/mbg/SurfVolTalk/svtalk.html html])
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**"Methods for the Generation and Analysis of Protein Simulations" (1995) ([http://bioinfo.mbb.yale.edu/hyper/mbg/SurfaceVolumes/sim-talk/sim-talk.ps.Z compressed postscript]) ([http://bioinfo.mbb.yale.edu/hyper/mbg/SurfaceVolumes/sim-talk/sim-talk.rtf rtf])
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== Other Resources ==
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== Other Stuff ==
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*[http://geometry.molmovdb.org/3dhmm Other Resources 3DHMM and Structural Alignment Code]
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*Picture [http://bioinfo.mbb.yale.edu/geometry/gallery.html gallery] (at [http://bioinfo.mbb.yale.edu/ bioinfo.mbb.yale.edu])
*Picture [http://bioinfo.mbb.yale.edu/geometry/gallery.html gallery] (at [http://bioinfo.mbb.yale.edu/ bioinfo.mbb.yale.edu])
*A [http://bioinfo.mbb.yale.edu/geometry/select.cgi script] for selecting parameter sets
*A [http://bioinfo.mbb.yale.edu/geometry/select.cgi script] for selecting parameter sets

Current revision

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 (fairly old)

Other Stuff

Personal tools