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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

A typical search result. nsSNP information is provided with structural information on the mutated amino acid residue—e.g. the secondary structure and solvent accessibility.
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Figure 2: A typical search result. nsSNP information is provided with structural information on the mutated amino acid residue—e.g. the secondary structure and solvent accessibility.

Mentions: As shown in Figure 2, the search result emerges with information about the mutation, the flanking amino acids, the secondary structure and the solvent accessibility of the mutated residue, allele frequency and heterozygosity. The output page also has a link to the original dbSNP database, enabling more detailed information to be obtained. If desired, the information can be saved in a flat text format for further analysis. The user can also easily observe the location of an nsSNP on the 3D protein structure by clicking either the ‘Download Structure’ link or the ‘Structure View’ box. We adopted two graphics programs, RasMol (http://openrasmol.org) and Jmol (http://jmol.sourceforge.net), for 3D protein visualization. The former is one of the most widely used software packages for visualizing the 3D structures of proteins and has a number of handy operations. The latter displays 3D structures in a Java-implemented browser.Figure 2.


coliSNP database server mapping nsSNPs on protein structures.

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

A typical search result. nsSNP information is provided with structural information on the mutated amino acid residue—e.g. the secondary structure and solvent accessibility.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 2: A typical search result. nsSNP information is provided with structural information on the mutated amino acid residue—e.g. the secondary structure and solvent accessibility.
Mentions: As shown in Figure 2, the search result emerges with information about the mutation, the flanking amino acids, the secondary structure and the solvent accessibility of the mutated residue, allele frequency and heterozygosity. The output page also has a link to the original dbSNP database, enabling more detailed information to be obtained. If desired, the information can be saved in a flat text format for further analysis. The user can also easily observe the location of an nsSNP on the 3D protein structure by clicking either the ‘Download Structure’ link or the ‘Structure View’ box. We adopted two graphics programs, RasMol (http://openrasmol.org) and Jmol (http://jmol.sourceforge.net), for 3D protein visualization. The former is one of the most widely used software packages for visualizing the 3D structures of proteins and has a number of handy operations. The latter displays 3D structures in a Java-implemented browser.Figure 2.

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