Cukuroglu Engin, Gursoy Attila, Nussinov Ruth, Keskin Ozlem
Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, Istanbul, Turkey.
National Cancer Institute, Cancer and Inflammation Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., National Cancer Institute, Frederick, Maryland, United States of America ; Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
PLoS One. 2014 Jan 27;9(1):e86738. doi: 10.1371/journal.pone.0086738. eCollection 2014.
Improvements in experimental techniques increasingly provide structural data relating to protein-protein interactions. Classification of structural details of protein-protein interactions can provide valuable insights for modeling and abstracting design principles. Here, we aim to cluster protein-protein interactions by their interface structures, and to exploit these clusters to obtain and study shared and distinct protein binding sites. We find that there are 22604 unique interface structures in the PDB. These unique interfaces, which provide a rich resource of structural data of protein-protein interactions, can be used for template-based docking. We test the specificity of these non-redundant unique interface structures by finding protein pairs which have multiple binding sites. We suggest that residues with more than 40% relative accessible surface area should be considered as surface residues in template-based docking studies. This comprehensive study of protein interface structures can serve as a resource for the community. The dataset can be accessed at http://prism.ccbb.ku.edu.tr/piface.
实验技术的改进越来越多地提供了与蛋白质-蛋白质相互作用相关的结构数据。蛋白质-蛋白质相互作用结构细节的分类可为建模和提取设计原则提供有价值的见解。在此，我们旨在根据蛋白质-蛋白质相互作用的界面结构对其进行聚类，并利用这些聚类来获取和研究共享的和不同的蛋白质结合位点。我们发现在蛋白质数据银行（PDB）中有22604种独特的界面结构。这些独特的界面提供了丰富的蛋白质-蛋白质相互作用结构数据资源，可用于基于模板的对接。我们通过寻找具有多个结合位点的蛋白质对来测试这些非冗余独特界面结构的特异性。我们建议在基于模板的对接研究中，相对可及表面积超过40%的残基应被视为表面残基。对蛋白质界面结构的这项全面研究可为学界提供一种资源。该数据集可在http://prism.ccbb.ku.edu.tr/piface获取。
