ColiSNP database server mapping nsSNPs on protein structures

Hidetoshi Kono, Tomo Yuasa, Shinya Nishiue, Kei Yura

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)D409-D413
JournalNucleic acids research
Volume36
Issue numberSUPPL. 1
DOIs
Publication statusPublished - 2008 Jan 1
Externally publishedYes

ASJC Scopus subject areas

  • Genetics

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