Kundrotas Petras J, Anishchenko Ivan, Dauzhenka Taras, Kotthoff Ian, Mnevets Daniil, Copeland Matthew M, Vakser Ilya A
Center for Computational Biology, The University of Kansas, Lawrence, Kansas, 66045.
Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas, 66045.
Protein Sci. 2018 Jan;27(1):172-181. doi: 10.1002/pro.3295. Epub 2017 Oct 10.
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resource (http://dockground.compbio.ku.edu) for structural modeling of protein interactions, including previously unpublished unbound docking benchmark set 4, and the X-ray docking decoy set 2.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.
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。实验测定的蛋白质-蛋白质复合物结构的数量仅占已知蛋白质相互作用的一小部分。相互作用组结构描述中的这一差距必须通过建模来弥合。蛋白质相互作用结构建模/对接技术发展的一个重要部分是蛋白质-蛋白质复合物数据库。它们对于研究蛋白质界面、为对接算法提供知识库以及开发分子间势、搜索程序和评分函数是必要的。蛋白质-蛋白质对接技术的发展需要在精心策划的蛋白质-蛋白质复合物集上对对接协议的不同部分进行全面的基准测试。我们全面描述了用于蛋白质相互作用结构建模的Dockground资源（http://dockground.compbio.ku.edu），包括之前未发表的未结合对接基准集4和X射线对接诱饵集2。该资源提供了各种相互关联的蛋白质-蛋白质复合物数据集以及其他数据，用于蛋白质对接方法不同方面的开发和测试。基于从PDB生物单元文件中提取的蛋白质-蛋白质复合物，Dockground提供了X射线未结合、模拟未结合、模型和对接诱饵结构集。所有数据集都可通过一个集成网站上的用户友好界面免费下载，可作为一个整体或选择特定结构进行下载。
