Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment
Authors: Lensink Marc F. , Brysbaert Guillaume , Nadzirin Nurul , Velankar Sameer , Chaleil Raphaël A. G. , Gerguri Tereza , Bates Paul A. , Laine Elodie , Carbone Alessandra , Grudinin Sergei , Kong Ren , Liu Ran‐Ran , Xu Xi‐Ming , Shi Hang , Chang Shan , Eisenstein Miriam , Karczynska Agnieszka , Czaplewski Cezary , Lubecka Emilia , Lipska Agnieszka , Krupa Paweł , Mozolewska Magdalena , Golon Łukasz , Samsonov Sergey , Liwo Adam , Crivelli Silvia , Pagès Guillaume , Karasikov Mikhail , Kadukova Maria , Yan Yumeng , Huang Sheng‐You , Rosell Mireia , Rodríguez‐Lumbreras Luis A. , Romero‐Durana Miguel , Díaz‐Bueno Lucía , Fernandez‐Recio Juan , Christoffer Charles , Terashi Genki , Shin Woong‐Hee , Aderinwale Tunde , Maddhuri Venkata Subraman Sai Raghavendra , Kihara Daisuke , Kozakov Dima , Vajda Sandor , Porter Kathryn , Padhorny Dzmitry , Desta Israel , Beglov Dmitri , Ignatov Mikhail , Kotelnikov Sergey , Moal Iain H. , Ritchie David W. , Chauvot de Beauchêne Isaure , Maigret Bernard , Devignes Marie‐Dominique , Ruiz Echartea Maria E. , Barradas‐Bautista Didier , Cao Zhen , Cavallo Luigi , Oliva Romina , Cao Yue , Shen Yang , Baek Minkyung , Park Taeyong , Woo Hyeonuk , Seok Chaok , Braitbard Merav , Bitton Lirane , Scheidman‐Duhovny Dina , Dapkūnas Justas , Olechnovič Kliment , Venclovas Česlovas , Kundrotas Petras J. , Belkin Saveliy , Chakravarty Devlina , Badal Varsha D. , Vakser Ilya A. , Vreven Thom , Vangaveti Sweta , Borrman Tyler , Weng Zhiping , Guest Johnathan D. , Gowthaman Ragul , Pierce Brian G. , Xu Xianjin , Duan Rui , Qiu Liming , Hou Jie , Ryan Merideth Benjamin , Ma Zhiwei , Cheng Jianlin , Zou Xiaoqin , Koukos Panagiotis I. , Roel‐Touris Jorge , Ambrosetti Francesco , Geng Cunliang , Schaarschmidt Jörg , Trellet Mikael E. , Melquiond Adrien S. J. , Xue Li , Jiménez‐García Brian , van Noort Charlotte W. , Honorato Rodrigo V. , Bonvin Alexandre M. J. J. , Wodak Shoshana J. 
Published: October 2019

AbstractWe present the results for CAPRI Round 46, the third joint CASP‐CAPRI protein assembly prediction challenge. The Round comprised a total of 20 targets including 14 homo‐oligomers and 6 heterocomplexes. Eight of the homo‐oligomer targets and one heterodimer comprised proteins that could be readily modeled using templates from the Protein Data Bank, often available for the full assembly. The remaining 11 targets comprised 5 homodimers, 3 heterodimers, and two higher‐order assemblies. These were more difficult to model, as their prediction mainly involved “ab‐initio” docking of subunit models derived from distantly related templates. A total of ~30 CAPRI groups, including 9 automatic servers, submitted on average ~2000 models per target. About 17 groups participated in the CAPRI scoring rounds, offered for most targets, submitting ~170 models per target. The prediction performance, measured by the fraction of models of acceptable quality or higher submitted across all predictors groups, was very good to excellent for the nine easy targets. Poorer performance was achieved by predictors for the 11 difficult targets, with medium and high quality models submitted for only 3 of these targets. A similar performance “gap” was displayed by scorer groups, highlighting yet again the unmet challenge of modeling the conformational changes of the protein components that occur upon binding or that must be accounted for in template‐based modeling. Our analysis also indicates that residues in binding interfaces were less well predicted in this set of targets than in previous Rounds, providing useful insights for directions of future improvements.