Non-redundant unique interface structures as templates for modeling protein interactions.
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.
Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, Istanbul, Turkey.
Engin
E
Cukuroglu
Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, Istanbul, Turkey.
Attila
A
Gursoy
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.
Ruth
R
Nussinov
Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, Istanbul, Turkey.
Ozlem
O
Keskin
D000465:Algorithms; D020134:Catalytic Domain / Q000235:genetics; D016000:Cluster Analysis; D030562:Databases, Protein / Q000706:statistics & numerical data; D006801:Humans; D008958:Models, Molecular; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D012984:Software