Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment

• DOI: 10.1002/prot.26609
• Publication Date: 2023-10-31T13:40:08Z
• Authors: Marc F. Lensink; Guillaume Brysbaert; Nessim Raouraoua; Paul A. Bates; Marco Giulini; Rodrigo V. Honorato; Charlotte van Noort; Joao M. C. Teixeira; Alexandre M. J. J...; Ren Kong; Hang Shi; Xufeng Lu; Shan Chang; Jian Liu; Zhiye Guo; Xiao Chen; Alex Morehead; Raj S. Roy; Tianqi Wu; Nabin Giri; Farhan Quadir; Chen Chen; Jianlin Cheng; Carlos A. Del Carpio; Eichiro Ichiishi; Luis A. Rodriguez...; Juan Fernandez‐Recio; Ameya Harmalkar; Lee‐Shin Chu; Sam Canner; Rituparna Smanta; Jeffrey J. Gray; Hao Li; Peicong Lin; Jiahua He; Huanyu Tao; Sheng‐You Huang; Jorge Roel‐Touris; Brian Jimenez‐Garcia; Charles W. Christ...; Anika J. Jain; Yuki Kagaya; Harini Kannan; Tsukasa Nakamura; Genki Terashi; Jacob C. Verburgt; Yuanyuan Zhang; Zicong Zhang; Hayato Fujuta; Masakazu Sekijima; Daisuke Kihara; Omeir Khan; Sergei Kotelnikov; Usman Ghani; Dzmitry Padhorny; Dmitri Beglov; Sandor Vajda; Dima Kozakov; Surendra S. Negi; Tiziana Ricciardelli; Didier Barradas‐B...; Zhen Cao; Mohit Chawla; Luigi Cavallo; Romina Oliva; Rui Yin; Melyssa Cheung; Johnathan D. Guest; Jessica Lee; Brian G. Pierce; Ben Shor; Tomer Cohen; Matan Halfon; Dina Schneidman‐D...; Shaowen Zhu; Rujie Yin; Yuanfei Sun; Yang Shen; Martyna Maszota‐Z...; Krzysztof K. Boja...; Emilia A. Lubecka; Mateusz Marcisz; Annemarie Danielsson; Lukasz Dziadek; Margrethe Gaardlos; Artur Gieldon; Adam Liwo; Sergey A. Samsonov; Rafal Slusarz; Karolina Zieba; Adam K. Sieradzan; Cezary Czaplewski; Shinpei Kobayashi; Yuta Miyakawa; Yasuomi Kiyota; Mayuko Takeda‐Shi...; Kliment Olechnovic; Lukas Valancauskas; Justas Dapkunas; Ceslovas Venclovas; Bjorn Wallner; Lin Yang; Chengyu Hou; Xiaodong He; Shuai Guo; Shenda Jiang; Xiaoliang Ma; Rui Duan; Liming Qui; Xianjin Xu; Xiaoqin Zou; Sameer Velankar; Shoshana J. Wodak
• Keywords: CASP

Abstract We present the results for CAPRI Round 54, 5th joint CASP‐CAPRI protein assembly prediction challenge. The offered 37 targets, including 14 homodimers, 3 homo‐trimers, 13 heterodimers antibody–antigen complexes, and 7 large assemblies. On average ~70 CASP predictor groups, more than 20 automatics servers, submitted models each target. A total of 21 941 by these groups 15 scorer were evaluated using model quality measures DockQ score consolidating measures. performance was quantified a weighted based on number acceptable or higher group among their five best models. Results show substantial progress achieved across significant fraction 60+ participating groups. High‐quality produced about 40% targets compared to 8% two years earlier. This remarkable improvement is due wide use AlphaFold2 AlphaFold2‐Multimer software confidence metrics they provide. Notably, expanded sampling candidate solutions manipulating deep learning inference engines, enriching multiple sequence alignments, integration advanced modeling tools, enabled top performing exceed standard version used as yard stick. notwithstanding, remained poor complexes with antibodies nanobodies, where evolutionary relationships between binding partners are lacking, featuring conformational flexibility, clearly indicating that remains challenging problem.