APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks.
APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks.
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DOI：
10.1093/nar/gkw363
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发表时间：
2016-07-08
影响因子：
14.9
通讯作者：
De Las Rivas J
中科院分区：
文献类型：
--
作者：
Alonso-López D;Gutiérrez MA;Lopes KP;Prieto C;Santamaría R;De Las Rivas J
APID(Agile Protein Interactomes DataServer)是一种交互式Web服务器，提供映射到各自蛋白质组的蛋白质交互的统一生成和传递。这个资源是一个新的、完全重新设计的服务器，它包括400多个生物(其中25个包括500多个相互作用)的蛋白质相互作用的全面集合，这些相互作用是通过整合仅经实验验证的蛋白质-蛋白质物理相互作用而产生的。对于每个蛋白质-蛋白质相互作用(PPI)，服务器包括当前报告的关于其实验验证的信息，以允许在不同的质量水平上进行选择和过滤。作为一个整体，它提供了从特定物种中轻松获取相互作用的途径，并包括一个由90,379种不同蛋白质和678,441种单一相互作用组成的全球统一概要。APID整合并统一了来自主要分子相互作用初级数据库、来自其他特定储存库的PPI，以及来自实验解析的蛋白质复合体3D结构的PPI，其中鉴定了两个以上的蛋白质。为此，对8,388个结构进行了分析，以确定具体的PPI。APID还包括一个新的图形工具(基于Cytoscape.js)，用于可视化和交互分析PPI网络。该服务器不需要注册，可在http://apid.dep.usal.es.上免费使用
APID (Agile Protein Interactomes DataServer) is an interactive web server that provides unified generation and delivery of protein interactomes mapped to their respective proteomes. This resource is a new, fully redesigned server that includes a comprehensive collection of protein interactomes for more than 400 organisms (25 of which include more than 500 interactions) produced by the integration of only experimentally validated protein–protein physical interactions. For each protein–protein interaction (PPI) the server includes currently reported information about its experimental validation to allow selection and filtering at different quality levels. As a whole, it provides easy access to the interactomes from specific species and includes a global uniform compendium of 90,379 distinct proteins and 678,441 singular interactions. APID integrates and unifies PPIs from major primary databases of molecular interactions, from other specific repositories and also from experimentally resolved 3D structures of protein complexes where more than two proteins were identified. For this purpose, a collection of 8,388 structures were analyzed to identify specific PPIs. APID also includes a new graph tool (based on Cytoscape.js) for visualization and interactive analyses of PPI networks. The server does not require registration and it is freely available for use at http://apid.dep.usal.es.