Surface Racer - Revision history

Christoph: /* External links */

2008-04-09T04:33:34Z

‎External links

Christoph: /* See also */

2007-07-17T04:43:42Z

‎See also

Christoph: /* References */

2007-04-27T22:17:59Z

‎References

Christoph at 04:07, 24 April 2007

2007-04-24T04:07:44Z

Christoph: /* See also */

2007-04-24T04:06:47Z

‎See also

Christoph at 04:03, 24 April 2007

2007-04-24T04:03:14Z

New page

'''Surface Racer''' calculates exact [[wikipedia:accessible surface area|accessible surface area]], molecular surface area, and average curvature of molecular surface for macromolecules. The program also analyzes cavities in the protein interior inaccessible from outside.<ref name="Tsodikov2002">Tsodikov OV, Record, Jr MT, Sergeev YV (2002). "A novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature". ''J Comput Chem, 23:600-609''.</ref>

==See also==
*[http://www.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html SURFNET] — generates surfaces and void regions between surfaces from coordinate data supplied in a PDB file.
*[http://wolf.bi.umist.ac.uk/naccess/ naccess]
*[http://www.cgl.ucsf.edu/Overview/software.html DMS] — compute molecular surfaces.
*[http://www.bioinformatics.leeds.ac.uk/ppi_pred/ PPI-Pred] — protein-protein interface prediction.
*[http://sumo-pbil.ibcp.fr/cgi-bin/sumo-welcome SuMo] — screen the Protein Data Bank (PDB) for finding ligand binding sites matching a protein structure or inversely, for finding protein structures matching a given site in a protein.
*[http://ligin.weizmann.ac.il/space/programs/ SPACE] — tools for Structure Prediction and Analysis based on Complementarity with Environment.
*[http://mgl.scripps.edu/people/sanner/html/msms_home.html MSMS] — compute very efficiently triangulations of Solvent Excluded Surfaces.
*[http://alpha2.bmc.uu.se/~gerard/manuals/voidoo.html VOIDOO Package] — a program for detection of cavities in macromolecular structures.
*[http://www.chem.utoronto.ca/staff/GAW/links.html sGAL] — software for finding surface exposed sites in proteins suitable for Cys-mediated cross-linking.

==References==
<references/>
===Further reading===
*Woolley GA, Lee E, Zhang F (2006). "sGAL: a computational method for finding surface exposed sites in proteins suitable for Cys-mediated cross-linking". ''Bioinformatics, 22(24):3101-3102''. {{doi|10.1093/bioinformatics/btl530}}.

[[Category:Bioinformatics]]

@@ Line 21: / Line 21: @@
 ==External links==
-*[http://monte.biochem.wisc.edu/~tsodikov/surface.html Surface Racer website]
+*[http://www.pharmacy.umich.edu/tsodikovlab/index_files/Page756.htm Surface Racer website]
 *[http://www.netsci.org/Science/Compchem/feature14e.html Network Science, Part 5: Solvent-Accessible Surfaces]
 [[Category:Bioinformatics]]

@@ Line 9: / Line 9: @@
 *[http://sumo-pbil.ibcp.fr/cgi-bin/sumo-welcome SuMo] &mdash; screen the Protein Data Bank (PDB) for finding ligand binding sites matching a protein structure or inversely, for finding protein structures matching a given site in a protein.
 *[http://ligin.weizmann.ac.il/space/programs/ SPACE] &mdash; tools for Structure Prediction and Analysis based on Complementarity with Environment.
-*[http://mgl.scripps.edu/people/sanner/html/msms_home.html MSMS] &mdash; compute very efficiently triangulations of Solvent Excluded Surfaces.
+*[[MSMS]] &mdash; compute very efficiently triangulations of Solvent Excluded Surfaces.
 *[http://alpha2.bmc.uu.se/~gerard/manuals/voidoo.html VOIDOO Package] &mdash; a program for detection of cavities in macromolecular structures.
 *[http://www.chem.utoronto.ca/staff/GAW/links.html sGAL] &mdash; software for finding surface exposed sites in proteins suitable for Cys-mediated cross-linking.

@@ Line 18: / Line 18: @@
 ===Further reading===
 *Woolley GA, Lee E, Zhang F (2006). "sGAL: a computational method for finding surface exposed sites in proteins suitable for Cys-mediated cross-linking". ''Bioinformatics, 22(24):3101-3102''. {{doi|10.1093/bioinformatics/btl530}}.
 ==External links==

@@ Line 2: / Line 2: @@
 ==See also==
 *[http://www.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html SURFNET] &mdash; generates surfaces and void regions between surfaces from coordinate data supplied in a PDB file.
 *[http://wolf.bi.umist.ac.uk/naccess/ naccess]
@@ Line 11: / Line 12: @@
 *[http://alpha2.bmc.uu.se/~gerard/manuals/voidoo.html VOIDOO Package] &mdash; a program for detection of cavities in macromolecular structures.
 *[http://www.chem.utoronto.ca/staff/GAW/links.html sGAL] &mdash; software for finding surface exposed sites in proteins suitable for Cys-mediated cross-linking.
 ==References==