Wang Yanli, Addess Kenneth J, Chen Jie, Geer Lewis Y, He Jane, He Siqian, Lu Shennan, Madej Thomas, Marchler-Bauer Aron, Thiessen Paul A, Zhang Naigong, Bryant Stephen H
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
Nucleic Acids Res. 2007 Jan;35(Database issue):D298-300. doi: 10.1093/nar/gkl952. Epub 2006 Nov 29.
Three-dimensional (3D) structure is now known for a large fraction of all protein families. Thus, it has become rather likely that one will find a homolog with known 3D structure when searching a sequence database with an arbitrary query sequence. Depending on the extent of similarity, such neighbor relationships may allow one to infer biological function and to identify functional sites such as binding motifs or catalytic centers. Entrez's 3D-structure database, the Molecular Modeling Database (MMDB), provides easy access to the richness of 3D structure data and its large potential for functional annotation. Entrez's search engine offers several tools to assist biologist users: (i) links between databases, such as between protein sequences and structures, (ii) pre-computed sequence and structure neighbors, (iii) visualization of structure and sequence/structure alignment. Here, we describe an annotation service that combines some of these tools automatically, Entrez's 'Related Structure' links. For all proteins in Entrez, similar sequences with known 3D structure are detected by BLAST and alignments are recorded. The 'Related Structure' service summarizes this information and presents 3D views mapping sequence residues onto all 3D structures available in MMDB (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=structure).
现在已知很大一部分蛋白质家族的三维（3D）结构。因此，当用任意查询序列搜索序列数据库时，很有可能找到具有已知3D结构的同源物。根据相似程度，这种邻域关系可能使人们能够推断生物学功能并识别功能位点，如结合基序或催化中心。Entrez的3D结构数据库，即分子建模数据库（MMDB），提供了对丰富的3D结构数据及其功能注释的巨大潜力的便捷访问。Entrez的搜索引擎提供了几种工具来协助生物学家用户：（i）数据库之间的链接，如蛋白质序列与结构之间的链接；（ii）预先计算的序列和结构邻域；（iii）结构以及序列/结构比对的可视化。在这里，我们描述一种自动结合其中一些工具的注释服务，即Entrez的“相关结构”链接。对于Entrez中的所有蛋白质，通过BLAST检测具有已知3D结构的相似序列并记录比对结果。“相关结构”服务总结这些信息，并呈现将序列残基映射到MMDB中所有可用3D结构上的3D视图（http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=structure）。
