ArchDB: automated protein loop classification as a tool for structural genomics
ArchDB: automated protein loop classification as a tool for structural genomics
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DOI：
10.1093/nar/gkh002
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发表时间：
2004-01-01
影响因子：
14.9
通讯作者：
Oliva, B
中科院分区：
文献类型：
--
作者：
Espadaler, J;Fernandez-Fuentes, N;Oliva, B
随着序列和结构基因组学计划的出现，蛋白质功能的注释已成为一个关键问题。大量证据表明，蛋白质结构信息经常编码在局部序列中，并且折叠主要由许多简单的超二级结构基序局部单元组成，由一些二级结构及其连接环组成。此外，蛋白质环在蛋白质功能中发挥着重要作用。在这里，我们介绍了 ArchDB，一种结构基序的分类数据库，由一个环及其支撑二级结构组成。 ArchDB 目前包含 12 665 个超二级元素，分为 1496 个主题子类。该数据库提供了一种简单的方法，可以从共享共同基序的蛋白质结构中检索功能信息，搜索在给定 SCOP 家族、超家族或折叠中发现的基序，或通过关键字搜索具有分类环的蛋白质。 ArchDB 循环数据库位于 http://sbi.imim.es/archdb。
The annotation of protein function has become a crucial problem with the advent of sequence and structural genomics initiatives. A large body of evidence suggests that protein structural information is frequently encoded in local sequences, and that folds are mainly made up of a number of simple local units of super-secondary structural motifs, consisting of a few secondary structures and their connecting loops. Moreover, protein loops play an important role in protein function. Here we present ArchDB, a classification database of structural motifs, consisting of one loop plus its bracing secondary structures. ArchDB currently contains 12 665 super-secondary elements classified into 1496 motif subclasses. The database provides an easy way to retrieve functional information from protein structures sharing a common motif, to search motifs found in a given SCOP family, superfamily or fold, or to search by keywords on proteins with classified loops. The ArchDB database of loops is located at http://sbi.imim.es/archdb.