ASTRAL compendium enhancements
ASTRAL compendium enhancements
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DOI：
10.1093/nar/30.1.260
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发表时间：
2002-01-01
影响因子：
14.9
通讯作者：
Brenner, SE
中科院分区：
文献类型：
--
作者：
Chandonia, JM;Walker, NS;Brenner, SE
ASTRAL纲要提供了几个数据库和工具，以帮助分析蛋白质结构，特别是通过使用它们的序列。它部分来自SCOP蛋白质结构域数据库，包括每个结构域的序列以及用于研究这些序列和结构域结构的其他资源。ASTRAL简编自2年前首次发布以来，已经进行了几项重大改进。包括的蛋白质结构域序列的数量翻了一番，从15190增加到30867，并增加了额外的数据库。快速访问格式（RAF）数据库包含手动管理的映射，该映射将PDB条目的SEQRES记录中描述的生物氨基酸序列链接到结构上观察到的氨基酸序列（在ATOM记录中提供），其格式旨在通过自动化工具快速访问。该信息用于推导SCOP数据库中蛋白质结构域的序列。在SCOP结构域跨越几条蛋白质链的情况下，所有这些蛋白质链都可以追溯到单个遗传来源，通过以原始基因序列中发现的顺序连接每条链的序列来创建“遗传结构域”序列。SCOP序列的原始样式文库和包括遗传结构域序列的新文库都是可用的。还包括基于多个标准和相似度的这些文库中的每一个的选择的代表性子集。ASTRAL可在www.example.com上访问。
The ASTRAL compendium provides several databases and tools to aid in the analysis of protein structures, particularly through the use of their sequences. It is partially derived from the SCOP database of protein domains, and it includes sequences for each domain as well as other resources useful for studying these sequences and domain structures. Several major improvements have been made to the ASTRAL compendium since its initial release 2 years ago. The number of protein domain sequences included has doubled from 15 190 to 30 867, and additional databases have been added. The Rapid Access Format (RAF) database contains manually curated mappings linking the biological amino acid sequences described in the SEQRES records of PDB entries to the amino acid sequences structurally observed (provided in the ATOM records) in a format designed for rapid access by automated tools. This information is used to derive sequences for protein domains in the SCOP database. In cases where a SCOP domain spans several protein chains, all of which can be traced back to a single genetic source, a 'genetic domain' sequence is created by concatenating the sequences of each chain in the order found in the original gene sequence. Both the original-style library of SCOP sequences and a new library including genetic domain sequences are available. Selected representative subsets of each of these libraries, based on multiple criteria and degrees of similarity, are also included. ASTRAL may be accessed at http://astral.stanford.edu/.