PIRSitePredict for protein functional site prediction using position-specific rules
PIRSitePredict for protein functional site prediction using position-specific rules
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DOI：
10.1093/database/baz026
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发表时间：
2019-02-26
影响因子：
5.8
通讯作者：
Wu, Cathy H.
中科院分区：
文献类型：
--
作者：
Chen, Chuming;Wang, Qinghua;Wu, Cathy H.
蛋白质的“全局”注释（如分子功能、生物学过程和家族中结构域或成员的存在）的预测方法已经达到了相对成熟的阶段。提供功能位点的细粒度“局部”注释（在单个氨基酸水平上）的方法现在正成为最前沿，特别是鉴于遗传变异数据的快速积累。我们已经开发了一种计算方法和工作流程，使用位置特异性条件模板注释规则（即PIR Site Rules或简称PIRSRs）预测蛋白质内的功能位点。这些规则是通过结构生物学家对已知蛋白质结构和其他实验数据的审查来策划的，并用于为UniProt知识库（UniProtKB）未审查部分生成高质量的注释。为了与更广泛的科学界分享PIRSR功能位点预测方法，我们简化了工作流程，并开发了一个名为PIRSitePredict的独立Java软件包。我们证明了使用PIRSitePredict的从头组装的基因组/转录组的功能注释注释的Trinity RNA-seq组装以下三种软骨鱼类的胚胎转录组的未表征的蛋白质：Leucoraja erinacea（小鳐），Scyliorhinus canicula（小斑点猫鲨）和Callorhinchus milii（象鲨）。每个物种平均预测约1200行注释。
Methods focused on predicting 'global' annotations for proteins (such as molecular function, biological process and presence of domains or membership in a family) have reached a relatively mature stage. Methods to provide fine-grained 'local' annotation of functional sites (at the level of individual amino acid) are now coming to the forefront, especially in light of the rapid accumulation of genetic variant data. We have developed a computational method and workflow that predicts functional sites within proteins using position-specific conditional template annotation rules (namely PIR Site Rules or PIRSRs for short). Such rules are curated through review of known protein structural and other experimental data by structural biologists and are used to generate high-quality annotations for the UniProt Knowledgebase (UniProtKB) unreviewed section. To share the PIRSR functional site prediction method with the broader scientific community, we have streamlined our workflow and developed a stand-alone Java software package named PIRSitePredict. We demonstrate the use of PIRSitePredict for functional annotation of de novo assembled genome/transcriptome by annotating uncharacterized proteins from Trinity RNA-seq assembly of embryonic transcriptomes of the following three cartilaginous fishes: Leucoraja erinacea (Little Skate), Scyliorhinus canicula (Small-spotted Catshark) and Callorhinchus milii (Elephant Shark). On average about 1200 lines of annotations were predicted for each species.