Article Dans Une Revue Nature Methods Année : 2024

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

Fan Bu (1, 2) , Yagoub Adam (3, 4) , Ryszard W Adamiak (5, 6) , Maciej Antczak (5, 6) , Belisa Rebeca H de Aquino (7) , Nagendar Goud Badepally (7) , Robert T Batey (8) , Eugene F Baulin (7) , Pawel Boinski (6) , Michal J Boniecki (7) , Janusz M Bujnicki (7) , Kristy A Carpenter (9) , Jose Chacon (10, 11) , Shi-Jie Chen (12) , Wah Chiu (13) , Pablo Cordero (10) , Naba Krishna Das (14) , Rhiju Das (10) , Wayne K Dawson (7) , Frank Dimaio (15) , Feng Ding (16) , Anne-Catherine Dock-Bregeon (17) , Nikolay V Dokholyan (18) , Ron O Dror (19, 20, 21, 22) , Stanisław Dunin-Horkawicz (7) , Stephan Eismann (23) , Eric Ennifar (24) , Reza Esmaeeli (25) , Masoud Amiri Farsani (7) , Adrian R Ferré-D’amaré (26) , Caleb Geniesse (10, 27) , George E Ghanim (28) , Horacio V Guzman (29) , Iris V Hood (30) , Lin Huang (31) , Dharm Skandh Jain (7) , Farhang Jaryani (7) , Lei Jin (12) , Astha Joshi (7) , Masha Karelina (19) , Jeffrey S Kieft (32, 33) , Wipapat Kladwang (10) , Sebastian Kmiecik (7) , Deepak Koirala (34) , Markus Kollmann (35) , Rachael C Kretsch (36) , Mateusz Kurciński (37) , Jun Li (12) , Shuang Li (30) , Marcin Magnus (7, 38) , Benoît Masquida (39) , S. Naeim Moafinejad (7) , Arup Mondal (25) , Sunandan Mukherjee (7) , Thi Hoang Duong Nguyen (40) , Grigory Nikolaev (7) , Chandran Nithin (7, 37) , Grace Nye (36) , Iswarya P N Pandaranadar Jeyeram (7) , Alberto Perez (25) , Phillip Pham (36) , Joseph A Piccirilli (41) , Smita Priyadarshini Pilla (7) , Radosław Pluta (7) , Simón Poblete (42) , Almudena Ponce-Salvatierra (7) , Mariusz Popenda (5) , Lukasz Popenda (43) , Fabrizio Pucci (44) , Ramya Rangan (36) , Angana Ray (7) , Aiming Ren (45) , Joanna Sarzynska (5) , Congzhou Mike Sha (18) , Filip Stefaniak (7) , Zhaoming Su (46) , Krishna C Suddala (30) , Marta Szachniuk (5, 6) , Raphael Townshend (19) , Robert J Trachman (26) , Jian Wang (18) , Wenkai Wang (47) , Andrew Watkins (10) , Tomasz K Wirecki (7) , Yi Xiao (48) , Peng Xiong (2, 49) , Yiduo Xiong (48) , Jianyi Yang (47) , Joseph David Yesselman (36, 50) , Jinwei Zhang (30) , Yi Zhang (48) , Zhenzhen Zhang (16) , Yuanzhe Zhou (12) , Tomasz Zok (6) , Dong Zhang (12) , Sicheng Zhang (12) , Adriana Żyła (7) , Eric Westhof (24, 51) , Zhichao Miao (1, 52, 53)
1 GMU - Guangzhou Medical University
2 USTC - University of Science and Technology of China [Hefei]
3 USP - Universidade de São Paulo = University of São Paulo
4 Covenant University
5 PAN - Polska Akademia Nauk = Polish Academy of Sciences = Académie polonaise des sciences
6 PUT - Poznan University of Technology
7 International Institute of Molecular and Cell Biology in Warsaw
8 University of Colorado [Boulder]
9 DBDS - Department of Biomedical Data Science [Stanford]
10 Department of Biochemistry [Stanford]
11 Cell and Developmental Biology [San Diego]
12 Mizzou - University of Missouri [Columbia]
13 Department of Bioengineering [Stanford]
14 UMBC - University of Maryland [Baltimore County]
15 Department of Biochemistry [Washington ]
16 Department of Physics and Astronomy [Clemson]
17 LBI2M - Laboratoire de Biologie Intégrative des Modèles Marins
18 Penn State College of Medicine
19 Computer Science Department [Stanford]
20 Department of Structural Biology [Stanford]
21 Department of Molecular and Cellular Physiology [Stanford]
22 ICME - Institute for Computational and Mathematical Engineering [Stanford]
23 Applied Physics Department [Stanford]
24 ARN - Architecture et Réactivité de l'ARN
25 UF - University of Florida [Gainesville]
26 NHLBI - National Heart, Lung, and Blood Institute [Bethesda]
27 LBNL - Lawrence Berkeley National Laboratory [Berkeley]
28 Laboratory of Molecular Biology [Cambridge]
29 UAM - Universidad Autónoma de Madrid
30 National Institute of Diabetes and Digestive and Kidney Diseases [Bethesda]
31 SYSU - Sun Yat-sen University [Guangzhou]
32 University of Colorado [Denver]
33 NYSBC - New York Structural Biology Center
34 University of Maryland [Baltimore]
35 Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf]
36 Stanford University
37 UW - University of Warsaw
38 Harvard University
39 GMGM - Génétique moléculaire, génomique, microbiologie
40 LMB - MRC Laboratory of Molecular Biology [Cambridge, UK]
41 UIC - University of Illinois [Chicago]
42 USS - Universidad San Sebastian = San Sebastian University [Santiago, Chile]
43 UAM - Uniwersytet im. Adama Mickiewicza w Poznaniu = Adam Mickiewicz University in Poznań
44 ULB - Université libre de Bruxelles
45 Zhejiang University [Hangzhou, China]
46 West China Hospital [Chengdu, Chine]
47 Shandong University
48 HUST - Huazhong University of Science and Technology [Wuhan]
49 University of Science & Technology of China [Suzhou]
50 University of Nebraska–Lincoln
51 UCAS - University of Chinese Academy of Sciences [Beijing]
52 Tongji University
53 Wellcome Trust Genome Campus
Robert T Batey
Wah Chiu
Rhiju Das
Frank Dimaio
Feng Ding
Nikolay V Dokholyan
Horacio V Guzman
Lin Huang
Masha Karelina
Deepak Koirala
Rachael C Kretsch
Jun Li
Grace Nye
  • Fonction : Auteur
Alberto Perez
Phillip Pham
  • Fonction : Auteur
Joseph A Piccirilli
Ramya Rangan
Aiming Ren
Congzhou Mike Sha
Jian Wang
Wenkai Wang
Jianyi Yang
Tomasz Zok

Résumé

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.

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Génétique
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hal-04907708 , version 1 (23-01-2025)

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Fan Bu, Yagoub Adam, Ryszard W Adamiak, Maciej Antczak, Belisa Rebeca H de Aquino, et al.. RNA-Puzzles Round V: blind predictions of 23 RNA structures. Nature Methods, 2024, ⟨10.1038/s41592-024-02543-9⟩. ⟨hal-04907708⟩
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