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Bioinformatics Advance Access published online on August 30, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn435
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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.

SNAP predicts effect of mutations on protein function

Yana Bromberg 1,2,*, Guy Yachdav 1,2 and Burkhard Rost 1,2,3

1Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, USA, 2Columbia University Center for Computational Biology and Bioinformatics (C2B2), 1130 St. Nicholas Ave. Rm. 802, New York, NY 10032, USA, and 3NorthEast Structural Genomics Consortium (NESG) and New York Consortium on Mem-brane Protein Structure (NYCOMPS), Columbia University, 1130 St. Nicholas Ave. Rm. 802, New York, NY 10032, USA

*To whom correspondence should be addressed. Dr.Yana Bromberg, E-mail: yana.bromberg{at}dbmi.columbia.edu, yb2009{at}columbia.edu


  Abstract

Summary: Many non-synonymous single nucleotide polymorphisms (nsSNPs) in humans are suspected to impact protein function. Here we present a publicly available server implementation of the method SNAP that predicts the functional effects of single amino acid substitutions. SNAP identifies over 80% of the non-neutral mutations at 77% accuracy and over 76% of the neutral mutations at 80% accuracy at its default threshold. Each prediction is associated with a reliability index that correlates with accuracy and thereby enables experimentalists to zoom into the most promising predictions.

Availability: Web-server: http://www.rostlab.org/services/SNAP; downloadable program available upon request.

Contact: bromberg{at}rostlab.org

Associate Editor: Alex Bateman

Received on May 29, 2008; revised on August 10, 2008; accepted on August 14, 2008

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