The ConSurf Server

	The ConSurf Server
	Server for the Identification of Functional Regions in Proteins
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Citing ConSurf and ConSurf Credits

In citing the ConSurf server please refer to

Ashkenazy H., Erez E., Martz E., Pupko T. and Ben-Tal N. 2010

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids.
Nucl. Acids Res. 2010; DOI: 10.1093/nar/gkq399; PMID: 20478830 [ABS],[PDF]

When using the server with protein structures (ConSurf method) please also refer to:

Landau M., Mayrose I., Rosenberg Y., Glaser F., Martz E., Pupko T. and Ben-Tal N. 2005.

ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures.
Nucl. Acids Res. 33:W299-W302. [ABS],[PDF]

Glaser F., Pupko T., Paz I., Bell R.E., Bechor D., Martz E. and Ben-Tal N. 2003.

ConSurf: Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information.
Bioinformatics 19:163-164. [ABS],[PDF]

When using the server with sequence only (ConSeq method) please also refer to:

Berezin C., Glaser F., Rosenberg J., Paz I., Pupko T., Fariselli P., Casadio R. and Ben-Tal N.
ConSeq: The Identification of Functionally and Structurally Important Residues in Protein Sequences.
Bioinformatics. Vol. 20 1322-1324, 2004. [PDF]

Main References

Mayrose I., Graur D., Ben-Tal N. and Pupko T. 2004.
Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior.
Mol. Biol. Evol. 21:1781-1791. PDF

Pupko T., Bell R.E., Mayrose I., Glaser F. and Ben-Tal N. 2002.
Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues.
Bioinformatics 18 Suppl 1:S71-S77. PDF
Armon A., Graur D. and Ben-Tal N. 2001.
ConSurf: An Algorithmic Tool for the Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information.
J. Mol. Biol. 307:447-463. PDF
Martz E. 2005.

FirstGlance in Jmol (firstglance.jmol.org)

Martz E. 2002.

Protein Explorer: easy yet powerful macromolecular visualization.
Trends in Biochemical Sciences.27:107-109. (PDF available on request.)

Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., and Ferrin, T.E.

UCSF Chimera - A Visualization System for Exploratory Research and Analysis.
J. Comput. Chem. 25(13):1605-1612 (2004).

Piero Fariselli and Rita Casadio.
RCNPRED: prediction of the residue co-ordination numbers in proteins.
Bioinformatics, 17, 202-204, 2001. (PDF)

Acknowledgements:

We are grateful to the Bioinformatics Unit, the Life-Science IT Unit and the George S. Wise Faculty of Life Sciences at Tel Aviv University for providing technical assistance and computation facilities.
The development was funded in part by Edmond J. Safra Center for Bioinformatics at Tel-Aviv university.
Development of Protein Explorer was supported by a grant to Eric Martz from the US National Science Foundation, Division of Undergraduate Education.

UCSF Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIH P41 RR-01081).

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