Impact of AlphaFold on Structure Prediction of Protein Complexes: The CASP15-CAPRI Experiment
Authors: Lensink Marc , Brysbaert Guillaume , Raouraoua Nessim , Bates Paul , Giulini Marco , Honorato Rodrigo Vargas , Noort Charlotte van , Teixeira João , Bonvin Alexandre M.J.J. , Kong Ren , Shi Hang , Lu Xufeng , Chang Shan , Liu Jian , Guo Zhiye , Chen Xiao , Morehead Alex , Roy Raj , Wu Tianqi , Giri Nabin , Quadir Farhan , Chen Chen , Cheng Jianlin , Carpio Carlos Del , Ichiishi Eichiro , A Luis Rodriguez-Lumbreras , Fernández-Recio Juan , Harmalkar Ameya , Chu Lee-Shin , Canner Sam , Smanta Rituparna , Gray Jeffrey , Li Hao , Lin Peicong , He Jiahua , Tao Huanyu , Huang Shengyou , Roel Jorge , Jimenez-Garcia Brian , Christoffer Charles , J Anika Jain , Kagaya Yuki , Kannan Harini , Nakamura Tsukasa , Terashi Genki , Verburgt Jacob , Zhang Yuanyuan , Zhang Zicong , Fujuta Hayato , Sekijima Masakazu , Kihara Daisuke , Khan Omeir , Kotelnikov Sergei , Ghani Usman , Padhorny Dzmitry , Beglov Dmitri , Vajda Sandor , Kozakov Dima , S Surendra Negi , Ricciardelli Tiziana , Barradas-Bautista Didier , Cao Zhen , Chawla Mohit , Cavallo Luigi , Oliva Romina , Yin Rui , Cheung Melyssa , Guest Johnathan , Lee Jessica , Pierce Brian , Shor Ben , Cohen Tomer , Halfon Matan , Schneidman-Duhovny Dina , Zhu Shaowen , Yin Rujie , Sun Yuanfei , Shen Yang , Maszota-Zieleniak Martyna , K Krzysztof Bojarski , Lubecka Emilia , Marcisz Mateusz , Danielsson Annemarie , Dziadek Lukasz , Gaardlos Margrethe , Giełdoń Artur , Liwo Jozef , Samsonov Sergey , Slusarz Rafal , Zieba Karolina , Sieradzan Adam , Czaplewski Cezary , Kobayashi Shinpei , Miyakawa Yuta , Kiyota Yasuomi , Takeda-Shitaka Mayuko , Olechnovič Kliment , Valančauskas Lukas , Dapkūnas Justas , Venclovas Ceslovas , Wallner Björn , Yang Lin , Hou Chengyu , He Xiaodong , Guo Shuai , Jiang Shenda , Ma Xiaoliang , Duan Rui , Qiu Liming , Xu Xianjin , Zou Xiaoqin , Velankar Sameer , J Shoshana Wodak 
Published: July 2023

We present the results for CAPRI Round 54, the 5th joint CASP-CAPRI
protein assembly prediction challenge. The Round offered 37 targets,
including 14 homo-dimers, 3 homo-trimers, 13 hetero-dimers including 3
antibody-antigen complexes, and 7 large assemblies. On average
~70 CASP and CAPRI predictor groups, including more than
20 automatics servers, submitted models for each target. A total of
21941 models submitted by these groups and by 15 CAPRI scorer groups
were evaluated using the CAPRI model quality measures and the DockQ
score consolidating these measures. The prediction performance was
quantified by a weighted score based on the number of models of
acceptable quality or higher submitted by each group among their 5 best
models. Results show substantial progress achieved across a significant
fraction of the 60+ participating groups. High-quality models were
produced for about 40% for the targets compared to 8% two years
earlier, a remarkable improvement resulting from the wide use of the
AlphaFold2 and AlphaFold-Multimer software. Creative use was made of the
deep learning inference engines affording the sampling of a much larger
number of models and enriching the multiple sequence alignments with
sequences from various sources. Wide use was also made of the AlphaFold
confidence metrics to rank models, permitting top performing groups to
exceed the results of the public AlphaFold-Multimer version used as a
yard stick. This notwithstanding, performance remained poor for
complexes with antibodies and nanobodies, where evolutionary
relationships between the binding partners are lacking, and for
complexes featuring conformational flexibility, clearly indicating that
the prediction of protein complexes remains a challenging problem.