TopoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association
TopoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association
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DOI：
10.1093/nar/gkh104
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发表时间：
2004-01-01
影响因子：
14.9
通讯作者：
Liang, J
中科院分区：
文献类型：
--
作者：
Stitziel, NO;Binkowski, TA;Liang, J
单核苷酸多态性（topopsnp）的地形测绘数据库为分析非同义snp （nssnp）提供了一个在线资源，这些非同义snp可以映射到已知的蛋白质3D结构上。其中包括来自人类在线孟德尔遗传（OMIM）数据库的疾病相关的非单核苷酸多态性，以及来自国家生物技术信息中心对单核苷酸多态性进行分类的资源dbSNP的其他非单核苷酸多态性。topopsnp进一步将每个nsSNP位点根据其几何位置分为三类：位于蛋白质表面口袋或内部空隙的位点，位于凸区或浅凹陷区的位点，以及完全埋藏在蛋白质结构内部的位点。这些独特的几何描述提供了更详细的nssnp到蛋白质结构的映射。当前版本还包括从Pfam数据库（蛋白质家族和保守蛋白基元数据库）获得的多个序列比对计算出的snp的相对熵，以及从ClustalW获得的手动调整的多个比对。这些结构和保守数据对于研究编码区域的nssnp是否可能导致表型变化是有用的。topopsnp包括一个交互式结构可视化web界面，以及可下载的批量数据。数据库将定期更新，可通过http:// gila.bioengr.uic.edu/snp/toposnp访问。
The database of topographic mapping of Single Nucleotide Polymorphism (topoSNP) provides an online resource for analyzing non-synonymous SNPs (nsSNPs) that can be mapped onto known 3D structures of proteins. These include disease-associated nsSNPs derived from the Online Mendelian Inheritance in Man (OMIM) database and other nsSNPs derived from dbSNP, a resource at the National Center for Biotechnology information that catalogs SNPs. TopoSNP further classifies each nsSNP site into three categories based on their geometric location: those located in a surface pocket or an interior void of the protein, those on a convex region or a shallow depressed region, and those that are completely buried in the interior of the protein structure. These unique geometric descriptions provide more detailed mapping of nsSNPs to protein structures. The current release also includes relative entropy of SNPs calculated from multiple sequence alignment as obtained from the Pfam database (a database of protein families and conserved protein motifs) as well as manually adjusted multiple alignments obtained from ClustalW. These structural and conservational data can be useful for studying whether nsSNPs in coding regions are likely to lead to phenotypic changes. TopoSNP includes an interactive structural visualization web interface, as well as downloadable batch data. The database will be updated at regular intervals and can be accessed at: http:// gila.bioengr.uic.edu/snp/toposnp.