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coliSNP database server mapping nsSNPs on protein structures.

Kono H, Yuasa T, Nishiue S, Yura K - Nucleic Acids Res. (2007)

Bottom Line: 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.

View Article: PubMed Central - PubMed

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

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.

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Related in: MedlinePlus

The coliSNP search interface. The user can use the protein section, SNP section or both to set the search conditions.
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Figure 1: The coliSNP search interface. The user can use the protein section, SNP section or both to set the search conditions.

Mentions: coliSNP can be accessed at http://yayoi.kansai.jaea.go.jp/colisnp. In the search form (Figure 1), a user can provide several search keys on the protein and/or the SNPs. In the protein section, the user can use as query terms the amino acid sequence, PDB ID, molecule name and keyword in PDB. The user can also limit the scope of the 3D protein structures to be mapped for SNPs by specifying the organisms that the proteins were derived from. In the SNP section, the user can give the organism, allele type and heterozygosity as queries. The user can also use both the protein and SNP sections to narrow the search.Figure 1.


coliSNP database server mapping nsSNPs on protein structures.

Kono H, Yuasa T, Nishiue S, Yura K - Nucleic Acids Res. (2007)

The coliSNP search interface. The user can use the protein section, SNP section or both to set the search conditions.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238833&req=5

Figure 1: The coliSNP search interface. The user can use the protein section, SNP section or both to set the search conditions.
Mentions: coliSNP can be accessed at http://yayoi.kansai.jaea.go.jp/colisnp. In the search form (Figure 1), a user can provide several search keys on the protein and/or the SNPs. In the protein section, the user can use as query terms the amino acid sequence, PDB ID, molecule name and keyword in PDB. The user can also limit the scope of the 3D protein structures to be mapped for SNPs by specifying the organisms that the proteins were derived from. In the SNP section, the user can give the organism, allele type and heterozygosity as queries. The user can also use both the protein and SNP sections to narrow the search.Figure 1.

Bottom Line: 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.

View Article: PubMed Central - PubMed

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

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.

Show MeSH
Related in: MedlinePlus