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.
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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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== Downloadable Software ==
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== Resources and Downloadable Software for Packing ==
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*[http://geometry.molmovdb.org/nucprot/ NucProt Site]
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*[http://www.molmovdb.org/cgi-bin/voronoi.cgi Packing-Eff Online]
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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://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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**libproteingeometry-2.3.1.tgz (full distribution v2.3.1) (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)
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**Windows binaries, src-diff (provided by Donald Gaffney at U Vermont)
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**[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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== Other Resources and Downloadable Software ==
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*[http://geometry.molmovdb.org/3dhmm/ 3D HMM] compares protein structures.
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*PGC: The Protein Geometry Calculator
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**[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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**Screenshots
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***[http://geometry.molmovdb.org/images/pgc/pgc-shot-01.png Some simple pgc expressions]
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***[http://geometry.molmovdb.org/images/pgc/pgc-shot-02.png Voronoi volumes for the residues a structure]
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== Documentation (fairly old) ==
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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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* [http://papers.gersteinlab.org/subject/volumes/index.html Papers on Volumes]
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* Old
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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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**"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 Stuff ==
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*Picture [http://bioinfo.mbb.yale.edu/geometry/gallery.html gallery] (at [http://bioinfo.mbb.yale.edu/ bioinfo.mbb.yale.edu])
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*A [http://bioinfo.mbb.yale.edu/geometry/select.cgi script] for selecting parameter sets
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*Related software packages at the [http://www.csb.yale.edu/ Center for Structural Biology] at Yale
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*[http://www.csb.yale.edu/userguides/datamanip/os/ OS]: Occluded surface and atomic packing
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*[http://www.csb.yale.edu/userguides/datamanip/volume/volume_descrip.html VOLUME]: Voronoi volumes software by F. M. Richards

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