title: coliSNP database server mapping nsSNPs on protein structures.
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.
authors.affiliation: Computational Biology Group, Quantum Beam Science Directorate, Japan Atomic Energy Agency, 8-1 Umemidai, Kizugawa, Kyoto 619-0215, PRESTO, Japan. kono.hidetoshi@jaea.go.jp
authors.forename: Hidetoshi
authors.initials: H
authors.lastname: Kono
authors.forename: Tomo
authors.initials: T
authors.lastname: Yuasa
authors.forename: Shinya
authors.initials: S
authors.lastname: Nishiue
authors.forename: Kei
authors.initials: K
authors.lastname: Yura
mesh_terms: D030561:Databases, Nucleic Acid; D030562:Databases, Protein; D006801:Humans; D020407:Internet; D020641:Polymorphism, Single Nucleotide; D017433:Protein Structure, Secondary; D011506:Proteins / Q000235:genetics*; D018511:Systems Integration; D014584:User-Computer Interface
chemical_list: D011506:Proteins