Difference between revisions of "Surface Racer"
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*[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://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://ligin.weizmann.ac.il/space/programs/ SPACE] — tools for Structure Prediction and Analysis based on Complementarity with Environment. | ||
| − | *[ | + | *[[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://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. | *[http://www.chem.utoronto.ca/staff/GAW/links.html sGAL] — software for finding surface exposed sites in proteins suitable for Cys-mediated cross-linking. | ||
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===Further reading=== | ===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}}. | *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}}. | ||
| + | *Jambon M (2006-08-10). "[http://wikiomics.org/wiki/Protein_volume Protein volume]". ''Wikiomics.org'' (accessed 2007-04-27). | ||
==External links== | ==External links== | ||
| − | *[http:// | + | *[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] | *[http://www.netsci.org/Science/Compchem/feature14e.html Network Science, Part 5: Solvent-Accessible Surfaces] | ||
[[Category:Bioinformatics]] | [[Category:Bioinformatics]] | ||
Latest revision as of 04:33, 9 April 2008
Surface Racer calculates exact 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.[1]
See also
- AREAIMOL is a command line tool in the CCP4 Program Suite for calculating ASA.
- SURFNET — generates surfaces and void regions between surfaces from coordinate data supplied in a PDB file.
- naccess
- DMS — compute molecular surfaces.
- PPI-Pred — protein-protein interface prediction.
- 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.
- SPACE — tools for Structure Prediction and Analysis based on Complementarity with Environment.
- MSMS — compute very efficiently triangulations of Solvent Excluded Surfaces.
- VOIDOO Package — a program for detection of cavities in macromolecular structures.
- sGAL — software for finding surface exposed sites in proteins suitable for Cys-mediated cross-linking.
- GETAREA — Solvent Accessible Surface Areas, Atomic Solvation Energies, and Their Gradients for Macromolecules.
References
- ↑ 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.
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 .
- Jambon M (2006-08-10). "Protein volume". Wikiomics.org (accessed 2007-04-27).
