RNA-Puzzles Round V: blind predictions of 23 RNA structures

作者：Fan Bu, Yagoub Adam, Ryszard W. Adamiak, Maciej Antczak, Belisa R. H. de Aquino, Nagendar Goud Badepally, Robert Batey, Eugene F. Baulin, Paweł Boiński, M. Boniecki, Janusz M. Bujnicki, Kristy A. Carpenter, Jose Chacon, Shi‐Jie Chen, Wah Chiu, Pablo Cordero, Naba Krishna Das, Rhiju Das, Wayne Dawson, Frank DiMaio, Feng Ding, Anne-Catherine Dock-Bregeon, Nikolay V. Dokholyan, Ron O. Dror, Stanisław Dunin-Horkawicz, Stephan Eismann, Eric Ennifar, Reza Esmaeeli, Masoud Amiri Farsani, A.R. Ferré-D′Amaré, Caleb Geniesse, George E. Ghanim, Horacio V. Guzman, Iris V. Hood, Lin Huang, Dharm Skandh Jain, Farhang Jaryani, Lei Jin, Astha Joshi, Masha Karelina, Jeffrey S. Kieft, Wipapat Kladwang, Sebastian Kmiecik, Deepak Koirala, Markus Kollmann, Rachael C. Kretsch, Mateusz Kurciński, Jun Li, Shuang Li, Marcin Magnus, Benoı̂t Masquida, S Naeim Moafinejad, Arup Mondal, Sunandan Mukherjee, Thi Hoang Duong Nguyen, Grigory I. Nikolaev, Chandran Nithin, Nye G, Iswarya P. N. Pandaranadar Jeyeram, Alberto Pérez, Phillip Pham, Joseph A. Piccirilli, Smita P. Pilla, Radosław Pluta, Simón Poblete, Almudena Ponce-Salvatierra, Mariusz Popenda, Łukasz Popenda, Fabrizio Pucci, Ramya Rangan, Angana Ray, Aiming Ren, Joanna Sarzyńska, Congzhou M. Sha, Filip Stefaniak, Zhaoming Su, Krishna C. Suddala, Marta Szachniuk, Raphael J.L. Townshend, Robert J. Trachman, Jian Wang, Wenkai Wang, Andrew M. Watkins, Tomasz Wirecki, Yi Xiao, Peng Xiong, Yiduo Xiong, Jianyi Yang, Joseph D. Yesselman, Jinwei Zhang, Yi Zhang, Zhenzhen Zhang, Yuanzhe Zhou, Tomasz Żok, Dong Zhang, Sicheng Zhang, Adriana Żyła, Éric Westhof, Zhichao Miao · 发表于：Nature Methods · 年份：2024 · DOI：10.1038/s41592-024-02543-9 · 被引用次数：66 · 研究领域：RNA and protein synthesis mechanisms、RNA modifications and cancer、Genomics and Phylogenetic Studies

RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA three-dimensional structure prediction. With agreement from structural biologists, RNA structures are predicted by modeling groups before publication of the experimental structures. We report a large-scale set of predictions by 18 groups for 23 RNA-Puzzles: 4 RNA elements, 2 Aptamers, 4 Viral elements, 5 Ribozymes and 8 Riboswitches. We describe automatic assessment protocols for comparisons between prediction and experiment. Our analyses reveal some critical steps to be overcome to achieve good accuracy in modeling RNA structures: identification of helix-forming pairs and of non-Watson-Crick modules, correct coaxial stacking between helices and avoidance of entanglements. Three of the top four modeling groups in this round also ranked among the top four in the CASP15 contest.