Manual classification strategies in the ECOD database.
Manual classification strategies in the ECOD database.
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DOI：
10.1002/prot.24818
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发表时间：
2015-07
期刊：
影响因子：
2.9
通讯作者：
Grishin NV
中科院分区：
文献类型：
--
作者：
Cheng H;Liao Y;Schaeffer RD;Grishin NV
蛋白质结构域进化分类（Evolutionary Classification Of Protein Domains）是一个全面的、最新的蛋白质结构分类数据库。每周从PDB（蛋白质数据库）发布的大多数新结构在ECOD层次结构中已经具有接近的同源物，因此可以可靠地划分为域并通过软件进行分类，而无需人工干预。然而，那些缺乏可靠的可检测同源物的蛋白质需要专家进行仔细分析。虽然许多生物信息学资源在某种程度上依赖于专家策展，但并不总是描述这种策展如何发生以及在什么情况下是必要的具体例子。在这里，我们举例说明人工分类策略在ECOD，集中在蛋白质分类的两个主要问题：域划分和同源性和相似性得分之间的关系。大多数示例显示最近发布的和手动分类的PDB结构。我们讨论了多结构域蛋白质，序列和结构相似性之间的不一致性，与分数评估同源性的困难，和完整的膜蛋白同源的可溶性蛋白质。通过及时将新的可用结构同化到其层次结构中，ECOD致力于提供最准确和最新的蛋白质结构世界视图，这是计算和专家驱动分析相结合的结果。
ECOD (Evolutionary Classification Of protein Domains) is a comprehensive and up-to-date protein structure classification database. The majority of new structures released from the PDB (Protein Data Bank) every week already have close homologs in the ECOD hierarchy and thus can be reliably partitioned into domains and classified by software without manual intervention. However, those proteins that lack confidently detectable homologs require careful analysis by experts. Although many bioinformatics resources rely on expert curation to some degree, specific examples of how this curation occurs and in what cases it is necessary are not always described. Here, we illustrate the manual classification strategy in ECOD by example, focusing on two major issues in protein classification: domain partitioning and the relationship between homology and similarity scores. Most examples show recently released and manually classified PDB structures. We discuss multi-domain proteins, discordance between sequence and structural similarities, difficulties with assessing homology with scores, and integral membrane proteins homologous to soluble proteins. By timely assimilation of newly available structures into its hierarchy, ECOD strives to provide a most accurate and updated view of the protein structure world as a result of combined computational and expert-driven analysis.