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

Fan Bu; Yagoub Adam; Ryszard W. Adamiak; Maciej Antczak; Belisa Rebeca H. de Aquino; Nagendar Goud Badepally; Robert T. Batey; Eugene F. Baulin; Pawel Boinski; Michal J. Boniecki; Janusz M. Bujnicki; Kristy A. Carpenter; Jose Chacon; Shi Jie Chen; Wah Chiu; Pablo Cordero; Naba Krishna Das; Rhiju Das; Wayne K. 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; Adrian 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; BenoÎt Masquida; S. Naeim Moafinejad; Arup Mondal; Sunandan Mukherjee; Thi Hoang Duong Nguyen; Grigory Nikolaev; Chandran Nithin; Grace Nye; Iswarya P.N. Pandaranadar Jeyeram; Alberto Perez; Phillip Pham; Joseph A. Piccirilli; Smita Priyadarshini Pilla; Radosław Pluta; Simón Poblete; Almudena Ponce-Salvatierra; Mariusz Popenda; Lukasz Popenda; Fabrizio Pucci; Ramya Rangan; Angana Ray; Aiming Ren; Joanna Sarzynska; Congzhou Mike Sha; Filip Stefaniak; Zhaoming Su; Krishna C. Suddala; Marta Szachniuk; Raphael Townshend; Robert J. Trachman; Jian Wang; Wenkai Wang; Andrew Watkins; Tomasz K. Wirecki; Yi Xiao; Peng Xiong; Yiduo Xiong; Jianyi Yang; Joseph David Yesselman; Jinwei Zhang; Yi Zhang; Zhenzhen Zhang; Yuanzhe Zhou; Tomasz Zok; Dong Zhang; Sicheng Zhang; Adriana Żyła; Eric Westhof; Zhichao Miao

doi:10.1038/s41592-024-02543-9

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

Fan Bu, Yagoub Adam, Ryszard W. Adamiak, Maciej Antczak, Belisa Rebeca H. de Aquino, Nagendar Goud Badepally, Robert T. Batey, Eugene F. Baulin, Pawel Boinski, Michal J. Boniecki, Janusz M. Bujnicki, Kristy A. Carpenter, Jose Chacon, Shi Jie Chen, Wah Chiu, Pablo Cordero, Naba Krishna Das, Rhiju Das, Wayne K. Dawson, Frank DiMaioFeng Ding, Anne Catherine Dock-Bregeon, Nikolay V. Dokholyan, Ron O. Dror, Stanisław Dunin-Horkawicz, Stephan Eismann, Eric Ennifar, Reza Esmaeeli, Masoud Amiri Farsani, Adrian 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, BenoÎt Masquida, S. Naeim Moafinejad, Arup Mondal, Sunandan Mukherjee, Thi Hoang Duong Nguyen, Grigory Nikolaev, Chandran Nithin, Grace Nye, Iswarya P.N. Pandaranadar Jeyeram, Alberto Perez, Phillip Pham, Joseph A. Piccirilli, Smita Priyadarshini Pilla, Radosław Pluta, Simón Poblete, Almudena Ponce-Salvatierra, Mariusz Popenda, Lukasz Popenda, Fabrizio Pucci, Ramya Rangan, Angana Ray, Aiming Ren, Joanna Sarzynska, Congzhou Mike Sha, Filip Stefaniak, Zhaoming Su, Krishna C. Suddala, Marta Szachniuk, Raphael Townshend, Robert J. Trachman, Jian Wang, Wenkai Wang, Andrew Watkins, Tomasz K. Wirecki, Yi Xiao, Peng Xiong, Yiduo Xiong, Jianyi Yang, Joseph David Yesselman, Jinwei Zhang, Yi Zhang, Zhenzhen Zhang, Yuanzhe Zhou, Tomasz Zok, Dong Zhang, Sicheng Zhang, Adriana Żyła, Eric Westhof, Zhichao Miao

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Abstract

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.

Original language	English (US)
Article number	2871
Pages (from-to)	399-411
Number of pages	13
Journal	Nature methods
Volume	22
Issue number	2
DOIs	https://doi.org/10.1038/s41592-024-02543-9
State	Published - Feb 2025

All Science Journal Classification (ASJC) codes

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

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10.1038/s41592-024-02543-9

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Bu, F., Adam, Y., Adamiak, R. W., Antczak, M., de Aquino, B. R. H., Badepally, N. G., Batey, R. T., Baulin, E. F., Boinski, P., Boniecki, M. J., Bujnicki, J. M., Carpenter, K. A., Chacon, J., Chen, S. J., Chiu, W., Cordero, P., Das, N. K., Das, R., Dawson, W. K., ... Miao, Z. (2025). RNA-Puzzles Round V: blind predictions of 23 RNA structures. Nature methods, 22(2), 399-411. Article 2871. https://doi.org/10.1038/s41592-024-02543-9

@article{c974d00f8e4c4fb2b7456a9f004b5996,

title = "RNA-Puzzles Round V: blind predictions of 23 RNA structures",

abstract = "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.",

author = "Fan Bu and Yagoub Adam and Adamiak, {Ryszard W.} and Maciej Antczak and {de Aquino}, {Belisa Rebeca H.} and Badepally, {Nagendar Goud} and Batey, {Robert T.} and Baulin, {Eugene F.} and Pawel Boinski and Boniecki, {Michal J.} and Bujnicki, {Janusz M.} and Carpenter, {Kristy A.} and Jose Chacon and Chen, {Shi Jie} and Wah Chiu and Pablo Cordero and Das, {Naba Krishna} and Rhiju Das and Dawson, {Wayne K.} and Frank DiMaio and Feng Ding and Dock-Bregeon, {Anne Catherine} and Dokholyan, {Nikolay V.} and Dror, {Ron O.} and Stanis{\l}aw Dunin-Horkawicz and Stephan Eismann and Eric Ennifar and Reza Esmaeeli and Farsani, {Masoud Amiri} and Ferr{\'e}-D{\textquoteright}Amar{\'e}, {Adrian R.} and Caleb Geniesse and Ghanim, {George E.} and Guzman, {Horacio V.} and Hood, {Iris V.} and Lin Huang and Jain, {Dharm Skandh} and Farhang Jaryani and Lei Jin and Astha Joshi and Masha Karelina and Kieft, {Jeffrey S.} and Wipapat Kladwang and Sebastian Kmiecik and Deepak Koirala and Markus Kollmann and Kretsch, {Rachael C.} and Mateusz Kurci{\'n}ski and Jun Li and Shuang Li and Marcin Magnus and Beno{\^I}t Masquida and Moafinejad, {S. Naeim} and Arup Mondal and Sunandan Mukherjee and Nguyen, {Thi Hoang Duong} and Grigory Nikolaev and Chandran Nithin and Grace Nye and {Pandaranadar Jeyeram}, {Iswarya P.N.} and Alberto Perez and Phillip Pham and Piccirilli, {Joseph A.} and Pilla, {Smita Priyadarshini} and Rados{\l}aw Pluta and Sim{\'o}n Poblete and Almudena Ponce-Salvatierra and Mariusz Popenda and Lukasz Popenda and Fabrizio Pucci and Ramya Rangan and Angana Ray and Aiming Ren and Joanna Sarzynska and Sha, {Congzhou Mike} and Filip Stefaniak and Zhaoming Su and Suddala, {Krishna C.} and Marta Szachniuk and Raphael Townshend and Trachman, {Robert J.} and Jian Wang and Wenkai Wang and Andrew Watkins and Wirecki, {Tomasz K.} and Yi Xiao and Peng Xiong and Yiduo Xiong and Jianyi Yang and Yesselman, {Joseph David} and Jinwei Zhang and Yi Zhang and Zhenzhen Zhang and Yuanzhe Zhou and Tomasz Zok and Dong Zhang and Sicheng Zhang and Adriana {\.Z}y{\l}a and Eric Westhof and Zhichao Miao",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2024.",

year = "2025",

month = feb,

doi = "10.1038/s41592-024-02543-9",

language = "English (US)",

volume = "22",

pages = "399--411",

journal = "Nature methods",

issn = "1548-7091",

publisher = "Nature Research",

number = "2",

}

Bu, F, Adam, Y, Adamiak, RW, Antczak, M, de Aquino, BRH, Badepally, NG, Batey, RT, Baulin, EF, Boinski, P, Boniecki, MJ, Bujnicki, JM, Carpenter, KA, Chacon, J, Chen, SJ, Chiu, W, Cordero, P, Das, NK, Das, R, Dawson, WK, DiMaio, F, Ding, F, Dock-Bregeon, AC, Dokholyan, NV, Dror, RO, Dunin-Horkawicz, S, Eismann, S, Ennifar, E, Esmaeeli, R, Farsani, MA, Ferré-D’Amaré, AR, Geniesse, C, Ghanim, GE, Guzman, HV, Hood, IV, Huang, L, Jain, DS, Jaryani, F, Jin, L, Joshi, A, Karelina, M, Kieft, JS, Kladwang, W, Kmiecik, S, Koirala, D, Kollmann, M, Kretsch, RC, Kurciński, M, Li, J, Li, S, Magnus, M, Masquida, B, Moafinejad, SN, Mondal, A, Mukherjee, S, Nguyen, THD, Nikolaev, G, Nithin, C, Nye, G, Pandaranadar Jeyeram, IPN, Perez, A, Pham, P, Piccirilli, JA, Pilla, SP, Pluta, R, Poblete, S, Ponce-Salvatierra, A, Popenda, M, Popenda, L, Pucci, F, Rangan, R, Ray, A, Ren, A, Sarzynska, J, Sha, CM, Stefaniak, F, Su, Z, Suddala, KC, Szachniuk, M, Townshend, R, Trachman, RJ, Wang, J, Wang, W, Watkins, A, Wirecki, TK, Xiao, Y, Xiong, P, Xiong, Y, Yang, J, Yesselman, JD, Zhang, J, Zhang, Y, Zhang, Z, Zhou, Y, Zok, T, Zhang, D, Zhang, S, Żyła, A, Westhof, E & Miao, Z 2025, 'RNA-Puzzles Round V: blind predictions of 23 RNA structures', Nature methods, vol. 22, no. 2, 2871, pp. 399-411. https://doi.org/10.1038/s41592-024-02543-9

TY - JOUR

T1 - RNA-Puzzles Round V

T2 - blind predictions of 23 RNA structures

AU - Bu, Fan

AU - Adam, Yagoub

AU - Adamiak, Ryszard W.

AU - Antczak, Maciej

AU - de Aquino, Belisa Rebeca H.

AU - Badepally, Nagendar Goud

AU - Batey, Robert T.

AU - Baulin, Eugene F.

AU - Boinski, Pawel

AU - Boniecki, Michal J.

AU - Bujnicki, Janusz M.

AU - Carpenter, Kristy A.

AU - Chacon, Jose

AU - Chen, Shi Jie

AU - Chiu, Wah

AU - Cordero, Pablo

AU - Das, Naba Krishna

AU - Das, Rhiju

AU - Dawson, Wayne K.

AU - DiMaio, Frank

AU - Ding, Feng

AU - Dock-Bregeon, Anne Catherine

AU - Dokholyan, Nikolay V.

AU - Dror, Ron O.

AU - Dunin-Horkawicz, Stanisław

AU - Eismann, Stephan

AU - Ennifar, Eric

AU - Esmaeeli, Reza

AU - Farsani, Masoud Amiri

AU - Ferré-D’Amaré, Adrian R.

AU - Geniesse, Caleb

AU - Ghanim, George E.

AU - Guzman, Horacio V.

AU - Hood, Iris V.

AU - Huang, Lin

AU - Jain, Dharm Skandh

AU - Jaryani, Farhang

AU - Jin, Lei

AU - Joshi, Astha

AU - Karelina, Masha

AU - Kieft, Jeffrey S.

AU - Kladwang, Wipapat

AU - Kmiecik, Sebastian

AU - Koirala, Deepak

AU - Kollmann, Markus

AU - Kretsch, Rachael C.

AU - Kurciński, Mateusz

AU - Li, Jun

AU - Li, Shuang

AU - Magnus, Marcin

AU - Masquida, BenoÎt

AU - Moafinejad, S. Naeim

AU - Mondal, Arup

AU - Mukherjee, Sunandan

AU - Nguyen, Thi Hoang Duong

AU - Nikolaev, Grigory

AU - Nithin, Chandran

AU - Nye, Grace

AU - Pandaranadar Jeyeram, Iswarya P.N.

AU - Perez, Alberto

AU - Pham, Phillip

AU - Piccirilli, Joseph A.

AU - Pilla, Smita Priyadarshini

AU - Pluta, Radosław

AU - Poblete, Simón

AU - Ponce-Salvatierra, Almudena

AU - Popenda, Mariusz

AU - Popenda, Lukasz

AU - Pucci, Fabrizio

AU - Rangan, Ramya

AU - Ray, Angana

AU - Ren, Aiming

AU - Sarzynska, Joanna

AU - Sha, Congzhou Mike

AU - Stefaniak, Filip

AU - Su, Zhaoming

AU - Suddala, Krishna C.

AU - Szachniuk, Marta

AU - Townshend, Raphael

AU - Trachman, Robert J.

AU - Wang, Jian

AU - Wang, Wenkai

AU - Watkins, Andrew

AU - Wirecki, Tomasz K.

AU - Xiao, Yi

AU - Xiong, Peng

AU - Xiong, Yiduo

AU - Yang, Jianyi

AU - Yesselman, Joseph David

AU - Zhang, Jinwei

AU - Zhang, Yi

AU - Zhang, Zhenzhen

AU - Zhou, Yuanzhe

AU - Zok, Tomasz

AU - Zhang, Dong

AU - Zhang, Sicheng

AU - Żyła, Adriana

AU - Westhof, Eric

AU - Miao, Zhichao

PY - 2025/2

Y1 - 2025/2

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85211438752&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85211438752&partnerID=8YFLogxK

U2 - 10.1038/s41592-024-02543-9

DO - 10.1038/s41592-024-02543-9

M3 - Article

C2 - 39623050

AN - SCOPUS:85211438752

SN - 1548-7091

VL - 22

SP - 399

EP - 411

JO - Nature methods

JF - Nature methods

IS - 2

M1 - 2871

ER -

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

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