Dockground: A comprehensive data resource for modeling of protein complexes
Dockground: A comprehensive data resource for modeling of protein complexes
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DOI：
10.1002/pro.3295
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发表时间：
2018-01-01
期刊：
影响因子：
8
通讯作者：
Vakser, Ilya A.
中科院分区：
文献类型：
--
作者：
Kundrotas, Petras J.;Anishchenko, Ivan;Vakser, Ilya A.
在分子水平上表征生命过程需要蛋白质相互作用的结构细节。实验确定的蛋白质-蛋白质复合物结构的数量只占已知蛋白质相互作用的一小部分。这种差距的结构描述的相互作用组必须通过建模来弥合。蛋白质相互作用的结构建模/对接技术的发展的一个重要组成部分是蛋白质-蛋白质复合物的数据库。它们对于研究蛋白质界面，为对接算法提供知识基础，以及开发分子间势能，搜索程序和评分功能是必要的。蛋白质-蛋白质对接技术的发展需要在精心策划的蛋白质-蛋白质复合物组上对对接协议的不同部分进行彻底的基准测试。我们提出了一个全面的描述Dockground资源（）的蛋白质相互作用的结构建模，包括以前未发表的未结合对接基准集4，和X射线对接诱饵集2。该资源提供了各种蛋白质-蛋白质复合物的互连数据集和其他数据，用于开发和测试蛋白质对接方法的不同方面。基于从PDB biounit文件中提取的蛋白质-蛋白质复合物，Dockground提供了一套X射线未结合，模拟未结合，模型和对接诱饵结构。所有数据集均可通过一个综合网站上的用户友好界面免费下载，可作为一个整体下载或选择特定结构下载。
Characterization of life processes at the molecular level requires structural details of protein interactions. The number of experimentally determined structures of protein-protein complexes accounts only for a fraction of known protein interactions. This gap in structural description of the interactome has to be bridged by modeling. An essential part of the development of structural modeling/docking techniques for protein interactions is databases of protein-protein complexes. They are necessary for studying protein interfaces, providing a knowledge base for docking algorithms, and developing intermolecular potentials, search procedures, and scoring functions. Development of protein-protein docking techniques requires thorough benchmarking of different parts of the docking protocols on carefully curated sets of protein-protein complexes. We present a comprehensive description of the Dockground resource () for structural modeling of protein interactions, including previously unpublished unbound docking benchmark set 4, and the X-ray docking decoy set 2. The resource offers a variety of interconnected datasets of protein-protein complexes and other data for the development and testing of different aspects of protein docking methodologies. Based on protein-protein complexes extracted from the PDB biounit files, Dockground offers sets of X-ray unbound, simulated unbound, model, and docking decoy structures. All datasets are freely available for download, as a whole or selecting specific structures, through a user-friendly interface on one integrated website.