Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: A CASP‐CAPRI experiment
Authors: Lensink Marc F. , Velankar Sameer , Kryshtafovych Andriy , Huang Shen‐You , Schneidman‐Duhovny Dina , Sali Andrej , Segura Joan , Fernandez‐Fuentes Narcis , Viswanath Shruthi , Elber Ron , Grudinin Sergei , Popov Petr , Neveu Emilie , Lee Hasup , Baek Minkyung , Park Sangwoo , Heo Lim , Rie Lee Gyu , Seok Chaok , Qin Sanbo , Zhou Huan‐Xiang , Ritchie David W. , Maigret Bernard , Devignes Marie‐Dominique , Ghoorah Anisah , Torchala Mieczyslaw , Chaleil Raphaël A.G. , Bates Paul A. , Ben‐Zeev Efrat , Eisenstein Miriam , Negi Surendra S. , Weng Zhiping , Vreven Thom , Pierce Brian G. , Borrman Tyler M. , Yu Jinchao , Ochsenbein Françoise , Guerois Raphaël , Vangone Anna , Rodrigues João P.G.L.M. , van Zundert Gydo , Nellen Mehdi , Xue Li , Karaca Ezgi , Melquiond Adrien S.J. , Visscher Koen , Kastritis Panagiotis L. , Bonvin Alexandre M.J.J. , Xu Xianjin , Qiu Liming , Yan Chengfei , Li Jilong , Ma Zhiwei , Cheng Jianlin , Zou Xiaoqin , Shen Yang , Peterson Lenna X. , Kim Hyung‐Rae , Roy Amit , Han Xusi , Esquivel‐Rodriguez Juan , Kihara Daisuke , Yu Xiaofeng , Bruce Neil J. , Fuller Jonathan C. , Wade Rebecca C. , Anishchenko Ivan , Kundrotas Petras J. , Vakser Ilya A. , Imai Kenichiro , Yamada Kazunori , Oda Toshiyuki , Nakamura Tsukasa , Tomii Kentaro , Pallara Chiara , Romero‐Durana Miguel , Jiménez‐García Brian , Moal Iain H. , Férnandez‐Recio Juan , Joung Jong Young , Kim Jong Yun , Joo Keehyoung , Lee Jooyoung , Kozakov Dima , Vajda Sandor , Mottarella Scott , Hall David R. , Beglov Dmitri , Mamonov Artem , Xia Bing , Bohnuud Tanggis , Del Carpio Carlos A. , Ichiishi Eichiro , Marze Nicholas , Kuroda Daisuke , Roy Burman Shourya S. , Gray Jeffrey J. , Chermak Edrisse , Cavallo Luigi , Oliva Romina , Tovchigrechko Andrey , Wodak Shoshana J. 
Published: April 2016

ABSTRACTWe present the results for CAPRI Round 30, the first joint CASP‐CAPRI experiment, which brought together experts from the protein structure prediction and protein–protein docking communities. The Round comprised 25 targets from amongst those submitted for the CASP11 prediction experiment of 2014. The targets included mostly homodimers, a few homotetramers, and two heterodimers, and comprised protein chains that could readily be modeled using templates from the Protein Data Bank. On average 24 CAPRI groups and 7 CASP groups submitted docking predictions for each target, and 12 CAPRI groups per target participated in the CAPRI scoring experiment. In total more than 9500 models were assessed against the 3D structures of the corresponding target complexes. Results show that the prediction of homodimer assemblies by homology modeling techniques and docking calculations is quite successful for targets featuring large enough subunit interfaces to represent stable associations. Targets with ambiguous or inaccurate oligomeric state assignments, often featuring crystal contact‐sized interfaces, represented a confounding factor. For those, a much poorer prediction performance was achieved, while nonetheless often providing helpful clues on the correct oligomeric state of the protein. The prediction performance was very poor for genuine tetrameric targets, where the inaccuracy of the homology‐built subunit models and the smaller pair‐wise interfaces severely limited the ability to derive the correct assembly mode. Our analysis also shows that docking procedures tend to perform better than standard homology modeling techniques and that highly accurate models of the protein components are not always required to identify their association modes with acceptable accuracy. Proteins 2016; 84(Suppl 1):323–348. © 2016 The Authors Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.