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Nucleic Acids Research Advance Access published online on October 16, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn716
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© 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.

Database Issue

SDR: a database of predicted specificity-determining residues in proteins

Jason E. Donald1,* and Eugene I. Shakhnovich2

1Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA and 2Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA

*To whom correspondence should be addressed. Tel: +617 893 8713; Fax: +215 573 7229; Email: jdon{at}mail.med.upenn.edu

Correspondence may also be addressed to Eugene I. Shakhnovich. Tel: +617 495 4130; Fax: +617 384 9228; Email: shakhnovich{at}chemistry.harvard.edu

Received August 6, 2008. Revised September 25, 2008. Accepted September 30, 2008.

The specificity-determining residue database (SDR database) presents residue positions where mutations are predicted to have changed protein function in large protein families. Because the database pre-calculates predictions on existing protein sequence alignments, users can quickly find the predictions by selecting the appropriate protein family or searching by protein sequence. Predictions can be used to guide mutagenesis or to gain a better understanding of specificity changes in a protein family. The database is available on the web at http://paradox.harvard.edu/sdr.


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