PIBASE: a comprehensive database of structurally defined protein interfaces
PIBASE: a comprehensive database of structurally defined protein interfaces
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DOI：
10.1093/bioinformatics/bti277
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发表时间：
2005-05-01
期刊：
影响因子：
5.8
通讯作者：
Sali, A
中科院分区：
文献类型：
--
作者：
Davis, FP;Sali, A
动机：近年来，蛋白质数据库（PDB）经历了快速增长。为了最大限度地利用存储在PDB中的高分辨率蛋白质-蛋白质相互作用数据，我们开发了PIBASE，一个全面的关系数据库，结构上定义的蛋白质结构域对之间的接口。它是由二进制接口提取的结构在PDB和可能的四级结构服务器使用结构域分配从蛋白质结构分类和CATH折叠classificationsystems.Results：PIBASE目前包含158 915相互作用的结构域对之间的105 061个结构域从2125 SCOP家庭。一组不同的几何，物理化学和拓扑性质计算每个复杂的，它的域，接口和结合位点。接口属性的子集用于删除PDB条目中的接口冗余，从而产生20 912个不同的域-域接口。复合物被分为989拓扑类的基础上，他们的模式域域接触。根据二级结构元素的拓扑结构，将二元界面及其相应的结合位点分别划分为18755和30975个拓扑类。该数据库的实用性说明了概述几个当前的应用程序。
Motivation: In recent years, the Protein Data Bank (PDB) has experienced rapid growth. To maximize the utility of the high resolution protein-protein interaction data stored in the PDB, we have developed PIBASE, a comprehensive relational database of structurally defined interfaces between pairs of protein domains. It is composed of binary interfaces extracted from structures in the PDB and the Probable Quaternary Structure server using domain assignments from the Structural Classification of Proteins and CATH fold classification systems.Results: PIBASE currently contains 158 915 interacting domain pairs between 105 061 domains from 2125 SCOP families. A diverse set of geometric, physiochemical and topologic properties are calculated for each complex, its domains, interfaces and binding sites. A subset of the interface properties are used to remove interface redundancy within PDB entries, resulting in 20 912 distinct domain-domain interfaces. The complexes are grouped into 989 topological classes based on their patterns of domain-domain contacts. The binary interfaces and their corresponding binding sites are categorized into 18 755 and 30 975 topological classes, respectively, based on the topology of secondary structure elements. The utility of the database is illustrated by outlining several current applications.