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Nucleic Acids Research Advance Access originally published online on October 29, 2008
Nucleic Acids Research 2009 37(Database issue):D323-D327; doi:10.1093/nar/gkn822
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Nucleic Acids Research, 2009, Vol. 37, Database issue D323-D327
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures

Ofir Goldenberg, Elana Erez, Guy Nimrod and Nir Ben-Tal*

Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel

*To whom correspondence should be addressed. Tel: +972-3-640-6709; Fax: +972-3-640-6834; Email: nirb{at}tauex.tau.ac.il

Received September 15, 2008. Revised October 12, 2008. Accepted October 13, 2008.

ConSurf-DB is a repository for evolutionary conservation analysis of the proteins of known structures in the Protein Data Bank (PDB). Sequence homologues of each of the PDB entries were collected and aligned using standard methods. The evolutionary conservation of each amino acid position in the alignment was calculated using the Rate4Site algorithm, implemented in the ConSurf web server. The algorithm takes into account the phylogenetic relations between the aligned proteins and the stochastic nature of the evolutionary process explicitly. Rate4Site assigns a conservation level for each position in the multiple sequence alignment using an empirical Bayesian inference. Visual inspection of the conservation patterns on the 3D structure often enables the identification of key residues that comprise the functionally important regions of the protein. The repository is updated with the latest PDB entries on a monthly basis and will be rebuilt annually. ConSurf-DB is available online at http://consurfdb.tau.ac.il/


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