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Associating Gene Ontology Terms with Pfam Protein Domains

机译:将基因本体论与PFAM蛋白域相关联

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With the growing number of three-dimensional protein structures in the protein data bank (PDB), there is a need to annotate these structures at the domain level in order to relate protein structure to protein function. Thanks to the SIFTS database, many PDB chains are now cross-referenced with Pfam domains and Gene ontology (GO) terms. However, these annotations do not include any explicit relationship between individual Pfam domains and GO terms. Therefore, creating a direct mapping between GO terms and Pfam domains will provide a new and more detailed level of protein structure annotation. This article presents a novel content-based filtering method called GODM that can automatically infer associations between GO terms and Pfam domains directly from existing GO-chain/Pfam-chain associations from the SIFTS database and GO-sequence/Pfam-sequence associations from the UniProt databases. Overall, GODM finds a total of 20,318 non-redundant GO-Pfam associations with a F-measure of 0.98 with respect to the InterPro database, which is treated here as a "Gold Standard". These associations could be used to annotate thousands of PDB chains or protein sequences for which their domain composition is known but which currently lack any GO annotation. The GODM database is publicly available at http://godm.loria.fr/.
机译:随着蛋白质数据库(PDB)中越来越多的三维蛋白质结构,需要在结构域水平下注释这些结构,以使蛋白质结构与蛋白质功能相关。由于SIFTS数据库,许多PDB链现已通过PFAM域和基因本体(GO)术语交叉引用。但是,这些注释不包括各个PFAM域之间的任何明确的关系和GO条款。因此,在GO术语和PFAM域之间创建直接映射将提供新的蛋白质结构注释水平。本文介绍了一种新的基于内容的滤波方法,称为云,可以直接从来自筛选数据库的现有的Go-Chain / Pfam-Chain关联与来自UniProt的Go-Chain / PFAM序列关联之间的Go条款和PFAM域之间的关联数据库。总的来说,众多关于Interproation数据库的F-Measure找到了20,318个非冗余的Go-PFAM关联,这是一个关于“黄金标准”。这些关联可用于注释千分之一的PDB链或蛋白质序列,其域组合物是已知的,但目前缺乏任何GO注释。 GoDM数据库在http://godm.loria.fr/上公开提供。

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