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Bioinformatics Advance Access originally published online on April 15, 2009
Bioinformatics 2009 25(11):1431-1432; doi:10.1093/bioinformatics/btp242
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures

Michael Ryan 1, Mark Diekhans 2, Stephanie Lien 3, Yun Liu 3 and Rachel Karchin 3,*

1Department of Bioinformatics, George Mason University, Fairfax, VA, 2Department of Biomolecular Engineering, University of California, Santa Cruz, CA and 3Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD, USA

*To whom correspondence should be addressed.


  Abstract

Summary: LS-SNP/PDB is a new WWW resource for genome-wide annotation of human non-synonymous (amino acid changing) SNPs. It serves high-quality protein graphics rendered with UCSF Chimera molecular visualization software. The system is kept up-to-date by an automated, high-throughput build pipeline that systematically maps human nsSNPs onto Protein Data Bank structures and annotates several biologically relevant features.

Availability: LS-SNP/PDB is available at http://ls-snp.icm.jhu.edu/ls-snp-pdb and via links from protein data bank (PDB) biology and chemistry tabs, UCSC Genome Browser Gene Details and SNP Details pages and PharmGKB Gene Variants Downloads/Cross-References pages.

Contact: karchin{at}jhu.edu

Supplementary Information: Supplementary data are available at Bioinformatics online.

Associate Editor: Dmitrij Frishman

Received on January 30, 2009; revised on March 12, 2009; accepted on April 3, 2009

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