Bu Fan, Adam Yagoub, Adamiak Ryszard W, Antczak Maciej, de Aquino Belisa Rebeca H, Badepally Nagendar Goud, Batey Robert T, Baulin Eugene F, Boinski Pawel, Boniecki Michal J, Bujnicki Janusz M, Carpenter Kristy A, Chacon Jose, Chen Shi-Jie, Chiu Wah, Cordero Pablo, Das Naba Krishna, Das Rhiju, Dawson Wayne K, DiMaio Frank, Ding Feng, Dock-Bregeon Anne-Catherine, Dokholyan Nikolay V, Dror Ron O, Dunin-Horkawicz Stanisław, Eismann Stephan, Ennifar Eric, Esmaeeli Reza, Farsani Masoud Amiri, Ferré-D'Amaré Adrian R, Geniesse Caleb, Ghanim George E, Guzman Horacio V, Hood Iris V, Huang Lin, Jain Dharm Skandh, Jaryani Farhang, Jin Lei, Joshi Astha, Karelina Masha, Kieft Jeffrey S, Kladwang Wipapat, Kmiecik Sebastian, Koirala Deepak, Kollmann Markus, Kretsch Rachael C, Kurciński Mateusz, Li Jun, Li Shuang, Magnus Marcin, Masquida BenoÎt, Moafinejad S Naeim, Mondal Arup, Mukherjee Sunandan, Nguyen Thi Hoang Duong, Nikolaev Grigory, Nithin Chandran, Nye Grace, Pandaranadar Jeyeram Iswarya P N, Perez Alberto, Pham Phillip, Piccirilli Joseph A, Pilla Smita Priyadarshini, Pluta Radosław, Poblete Simón, Ponce-Salvatierra Almudena, Popenda Mariusz, Popenda Lukasz, Pucci Fabrizio, Rangan Ramya, Ray Angana, Ren Aiming, Sarzynska Joanna, Sha Congzhou Mike, Stefaniak Filip, Su Zhaoming, Suddala Krishna C, Szachniuk Marta, Townshend Raphael, Trachman Robert J, Wang Jian, Wang Wenkai, Watkins Andrew, Wirecki Tomasz K, Xiao Yi, Xiong Peng, Xiong Yiduo, Yang Jianyi, Yesselman Joseph David, Zhang Jinwei, Zhang Yi, Zhang Zhenzhen, Zhou Yuanzhe, Zok Tomasz, Zhang Dong, Zhang Sicheng, Żyła Adriana, Westhof Eric, Miao Zhichao
GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macao Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China.
School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
Nat Methods. 2025 Feb;22(2):399-411. doi: 10.1038/s41592-024-02543-9. Epub 2024 Dec 2.
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.
RNA难题计划是一项致力于推动和改进RNA三维结构预测的集体行动。经结构生物学家同意，在实验结构发表之前，由建模团队对RNA结构进行预测。我们报告了18个团队对23个RNA难题的大规模预测结果：4个RNA元件、2个适体、4个病毒元件、5个核酶和8个核糖开关。我们描述了用于预测与实验比较的自动评估方案。我们的分析揭示了在RNA结构建模中要达到高精度需要克服的一些关键步骤：识别形成螺旋的碱基对和非沃森-克里克模块、螺旋之间正确的同轴堆积以及避免缠结。本轮排名前四的建模团队中有三个在第15届蛋白质结构预测关键评估（CASP15）竞赛中也排名前四。
