AraPPISite: a database of fine-grained protein-protein interaction site annotations for Arabidopsis thaliana
AraPPISite: a database of fine-grained protein-protein interaction site annotations for Arabidopsis thaliana
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AraPPISite：拟南芥细粒度蛋白质-蛋白质相互作用位点注释数据库
DOI：
10.1007/s11103-016-0498-z
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发表时间：
2016-09-01
影响因子：
5.1
通讯作者：
Zhang，Ziding
中科院分区：
文献类型：
--
作者：
Li，Hong;Yang，Shiping;Zhang，Ziding
有关蛋白质相互作用位点的知识提供了蛋白质-蛋白质相互作用 (PPI) 的详细信息。迄今为止，已鉴定出近 20,000 种来自拟南芥的 PPI。然而，先前发布的 PPI 数据库很大程度上遗漏了交互位点信息。这里是 AraPPISite，一个提供 A 的细粒度交互细节的数据库。 thalianaPPIs 成立。首先，通过实验确定27A的3D结构。 thalianaPPIs 是从蛋白质数据库数据库和 3023A 的预测 3D 结构中收集的。 thalianaPPIs 使用两种成熟的基于模板的对接方法进行建模。对于每一个实验/预测的复杂结构，AraPPISite不仅提供了用于浏览交互位点的交互式用户界面，还列出了这些位点的详细进化和理化特性。其次，AraPPISite 将域-域交互或域-基序交互分配给 4286 个 3D 结构无法建模的 PPI。在这种情况下，用户可以轻松地在序列水平上查询蛋白质相互作用区域。 AraPPISite 是一个免费且用户友好的数据库，不需要用户注册或在本地计算机上进行任何配置。我们预计AraPPISite可以作为结构生物学或蛋白质生物信息学经验较少的用户的有用数据库资源来探究PPI的细节，从而加速植物遗传学和功能基因组学的研究。 AraPPISite 位于 http://systbio.cau.edu.cn/arappisite/index.html 。
Knowledge about protein interaction sites provides detailed information of protein–protein interactions (PPIs). To date, nearly 20,000 of PPIs fromArabidopsis thalianahave been identified. Nevertheless, the interaction site information has been largely missed by previously published PPI databases. Here, AraPPISite, a database that presents fine-grained interaction details forA. thalianaPPIs is established. First, the experimentally determined 3D structures of 27A. thalianaPPIs are collected from the Protein Data Bank database and the predicted 3D structures of 3023A. thalianaPPIs are modeled by using two well-established template-based docking methods. For each experimental/predicted complex structure, AraPPISite not only provides an interactive user interface for browsing interaction sites, but also lists detailed evolutionary and physicochemical properties of these sites. Second, AraPPISite assigns domain–domain interactions or domain–motif interactions to 4286 PPIs whose 3D structures cannot be modeled. In this case, users can easily query protein interaction regions at the sequence level. AraPPISite is a free and user-friendly database, which does not require user registration or any configuration on local machines. We anticipate AraPPISite can serve as a helpful database resource for the users with less experience in structural biology or protein bioinformatics to probe the details of PPIs, and thus accelerate the studies of plant genetics and functional genomics. AraPPISite is available at http://systbio.cau.edu.cn/arappisite/index.html .