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Nucleic Acids Research Advance Access published online on October 5, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm801
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© 2007 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

coliSNP database server mapping nsSNPs on protein structures

Hidetoshi Kono1,2,3,*, Tomo Yuasa4, Shinya Nishiue5 and Kei Yura3,6

1Computational Biology Group, Quantum Beam Science Directorate, Japan Atomic Energy Agency, 8-1 Umemidai, Kizugawa, Kyoto 619-0215, 2PRESTO, Japan Science and Technology Agency, 4-1-8 Kawaguchi, Saitama, 332-0012, 3Research Unit for Quantum Beam Life Science Initiative, Quantum Beam Science Directorate, Japan Atomic Energy Agency, 8-1 Umemidai, Kizugawa, Kyoto 619-0215, 4Bioinformatics Department, Mitsubishi Space Software CO. LTD, 5-4-36 Tsukaguchi-honmachi, Amagasaki, Hyogo 661-0001, 5Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188 and 6Quantum Bioinformatics Team, Center for Computational Science and Engineering, Japan Atomic Energy Agency, 8-1 Umemidai, Kizugawa, Kyoto 619-0215 Japan

*To whom correspondence should be addressed. Tel: +81-774-71-3465; Fax: +81-774-71-3460; Email: kono.hidetoshi{at}jaea.go.jp

Received August 15, 2007. Revised September 13, 2007. Accepted September 17, 2007.

We have developed coliSNP, a database server (http://yayoi.kansai.jaea.go.jp/colisnp) that maps non-synonymous single nucleotide polymorphisms (nsSNPs) on the three-dimensional (3D) structure of proteins. Once a week, the SNP data from the dbSNP database and the protein structure data from the Protein Data Bank (PDB) are downloaded, and the correspondence of the two data sets is automatically tabulated in the coliSNP database. Given an amino acid sequence, protein name or PDB ID, the server will immediately provide known nsSNP information, including the amino acid mutation caused by the nsSNP, the solvent accessibility, the secondary structure and the flanking residues of the mutated residue in a single page. The position of the nsSNP within the amino acid sequence and on the 3D structure of the protein can also be observed. The database provides key information with which to judge whether an observed nsSNP critically affects protein function and/or stability. As far as we know, this is the only web-based nsSNP database that automatically compiles SNP and protein information in a concise manner.


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