ECDomainMiner: discovering hidden associations between enzyme commission numbers and Pfam domains.
ECDomainMiner: discovering hidden associations between enzyme commission numbers and Pfam domains.
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DOI：
10.1186/s12859-017-1519-x
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发表时间：
2017-02-13
影响因子：
3
通讯作者：
Ritchie DW
中科院分区：
文献类型：
--
作者：
Alborzi SZ;Devignes MD;Ritchie DW
蛋白质数据库（PDB）中的许多条目都根据Pfam分类进行了注释，以显示其组成蛋白结构域，并通过酶委员会（EC）编号方案显示其生物学功能。然而，尽管许多蛋白质的生物活性通常来自特定的结构域-结构域和结构域-配体相互作用，但目前的在线资源很少提供结构域水平上从结构到功能的直接映射。由于PDB现在包含数以万计的蛋白质链，并且由于蛋白质序列数据库可以使这些数字缩小几个数量级，因此迫切需要开发可以在结构域级别操作的自动结构-功能注释工具。本文介绍了ECDomainMiner，这是一种新颖的基于内容的过滤方法，可以自动推断EC编号和Pfam域之间的关联。ECDomainMiner发现，相对于从InterPro提取的“金标准”测试集，总共有20,728个非冗余EC-Pfam关联，f值为0.95。与InterPro中1515个手动管理的EC-Pfam协会相比，ECDomainMiner推断EC-Pfam协会的数量增加了13倍。这些EC- pfam关联可用于注释PDB中目前缺乏EC注释的58,722个蛋白链。ECDomainMiner数据库可在http://ecdm.loria.fr/上公开获取。
Many entries in the protein data bank (PDB) are annotated to show their component protein domains according to the Pfam classification, as well as their biological function through the enzyme commission (EC) numbering scheme. However, despite the fact that the biological activity of many proteins often arises from specific domain-domain and domain-ligand interactions, current on-line resources rarely provide a direct mapping from structure to function at the domain level. Since the PDB now contains many tens of thousands of protein chains, and since protein sequence databases can dwarf such numbers by orders of magnitude, there is a pressing need to develop automatic structure-function annotation tools which can operate at the domain level. This article presents ECDomainMiner, a novel content-based filtering approach to automatically infer associations between EC numbers and Pfam domains. ECDomainMiner finds a total of 20,728 non-redundant EC-Pfam associations with a F-measure of 0.95 with respect to a “Gold Standard” test set extracted from InterPro. Compared to the 1515 manually curated EC-Pfam associations in InterPro, ECDomainMiner infers a 13-fold increase in the number of EC-Pfam associations. These EC-Pfam associations could be used to annotate some 58,722 protein chains in the PDB which currently lack any EC annotation. The ECDomainMiner database is publicly available at http://ecdm.loria.fr/.