Nucleic Acids Research Advance Access published online on May 13, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp339
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Web Server Issue |
INTREPID: a web server for prediction of functionally important residues by evolutionary analysis
1Department of Computer Science, 2Department of Bioengineering and 3Department of Plant and Microbial Biology, University of California, Berkeley, USA
*To whom correspondence should be addressed. Tel: +1 510 642 9932; Fax: +1 510 642 5835; Email: kimmen{at}berkeley.edu
Received March 3, 2009. Revised April 13, 2009. Accepted April 21, 2009.
We present the INTREPID web server for predicting functionally important residues in proteins. INTREPID has been shown to boost the recall and precision of catalytic residue prediction over other sequence-based methods and can be used to identify other types of functional residues. The web server takes an input protein sequence, gathers homologs, constructs a multiple sequence alignment and phylogenetic tree and finally runs the INTREPID method to assign a score to each position. Residues predicted to be functionally important are displayed on homologous 3D structures (where available), highlighting spatial patterns of conservation at various significance thresholds. The INTREPID web server is available at http://phylogenomics.berkeley.edu/intrepid.