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

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dc.contributor.authorBu, Fan
dc.contributor.authorAdam, Yagoub
dc.contributor.authorAdamiak, Ryszard W.
dc.contributor.authorAntczak, Maciej
dc.contributor.authorde Aquino, Belisa Rebeca H.
dc.contributor.authorBadepally, Nagendar Goud
dc.contributor.authorBatey, Robert T.
dc.contributor.authorBaulin, Eugene F.
dc.contributor.authorBoinski, Pawel
dc.contributor.authorBoniecki, Michal J.
dc.contributor.authorBujnicki, Janusz M.
dc.contributor.authorCarpenter, Kristy A.
dc.contributor.authorChacon, Jose
dc.contributor.authorChen, Shi-Jie
dc.contributor.authorChiu, Wah
dc.contributor.authorCordero, Pablo
dc.contributor.authorDas, Naba Krishna
dc.contributor.authorDas, Rhiju
dc.contributor.authorDawson, Wayne K.
dc.contributor.authorDiMaio, Frank
dc.contributor.authorDing, Feng
dc.contributor.authorDock-Bregeon, Anne-Catherine
dc.contributor.authorDokholyan, Nikolay V.
dc.contributor.authorDror, Ron O.
dc.contributor.authorDunin-Horkawicz, Stanisław
dc.contributor.authorEismann, Stephan
dc.contributor.authorEnnifar, Eric
dc.contributor.authorEsmaeeli, Reza
dc.contributor.authorFarsani, Masoud Amiri
dc.contributor.authorFerré-D’Amaré, Adrian R.
dc.contributor.authorGeniesse, Caleb
dc.contributor.authorGhanim, George E.
dc.contributor.authorGuzman, Horacio V.
dc.contributor.authorHood, Iris V.
dc.contributor.authorHuang, Lin
dc.contributor.authorJain, Dharm Skandh
dc.contributor.authorJaryani, Farhang
dc.contributor.authorJin, Lei
dc.contributor.authorJoshi, Astha
dc.contributor.authorKarelina, Masha
dc.contributor.authorKieft, Jeffrey S.
dc.contributor.authorKladwang, Wipapat
dc.contributor.authorKmiecik, Sebastian
dc.contributor.authorKoirala, Deepak
dc.contributor.authorKollmann, Markus
dc.contributor.authorKretsch, Rachael C.
dc.contributor.authorKurciński, Mateusz
dc.contributor.authorLi, Jun
dc.contributor.authorLi, Shuang
dc.contributor.authorMagnus, Marcin
dc.contributor.authorMasquida, BenoÎt
dc.contributor.authorMoafinejad, S. Naeim
dc.contributor.authorMondal, Arup
dc.contributor.authorMukherjee, Sunandan
dc.contributor.authorNguyen, Thi Hoang Duong
dc.contributor.authorNikolaev, Grigory
dc.contributor.authorNithin, Chandran
dc.contributor.authorNye, Grace
dc.contributor.authorPandaranadar Jeyeram, Iswarya P. N.
dc.contributor.authorPerez, Alberto
dc.contributor.authorPham, Phillip
dc.contributor.authorPiccirilli, Joseph A.
dc.contributor.authorPilla, Smita Priyadarshini
dc.contributor.authorPluta, Radosław
dc.contributor.authorPoblete, Simón
dc.contributor.authorPonce-Salvatierra, Almudena
dc.contributor.authorPopenda, Mariusz
dc.contributor.authorPopenda, Lukasz
dc.contributor.authorPucci, Fabrizio
dc.contributor.authorRangan, Ramya
dc.contributor.authorRay, Angana
dc.contributor.authorRen, Aiming
dc.contributor.authorSarzynska, Joanna
dc.contributor.authorSha, Congzhou Mike
dc.contributor.authorStefaniak, Filip
dc.contributor.authorSu, Zhaoming
dc.contributor.authorSuddala, Krishna C.
dc.contributor.authorSzachniuk, Marta
dc.contributor.authorTownshend, Raphael
dc.contributor.authorTrachman, Robert J.
dc.contributor.authorWang, Jian
dc.contributor.authorWang, Wenkai
dc.contributor.authorWatkins, Andrew
dc.contributor.authorWirecki, Tomasz K.
dc.contributor.authorXiao, Yi
dc.contributor.authorXiong, Peng
dc.contributor.authorXiong, Yiduo
dc.contributor.authorYang, Jianyi
dc.contributor.authorYesselman, Joseph David
dc.contributor.authorZhang, Jinwei
dc.contributor.authorZhang, Yi
dc.contributor.authorZhang, Zhenzhen
dc.contributor.authorZhou, Yuanzhe
dc.contributor.authorZok, Tomasz
dc.contributor.authorZhang, Dong
dc.contributor.authorZhang, Sicheng
dc.contributor.authorŻyła, Adriana
dc.contributor.authorWesthof, Eric
dc.contributor.authorMiao, Zhichao
dc.date.accessioned2025-02-13T17:56:23Z
dc.date.available2025-02-13T17:56:23Z
dc.date.issued2024-12-02
dc.description.abstractRNA-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.
dc.description.sponsorshipZ.M. is supported by Major Projects of Guangzhou National Laboratory (grant no. GZNL2023A01006, GZNL2024A01002, SRPG22-003, SRPG22-006, SRPG22-007, HWYQ23-003 and YW-YFYJ0102), the Natural Science Foundation of China (32270707) and the National Key R&D Programs of China (2023YFF1204700, 2023YFF1204701, 2021YFF1200900 and 2021YFF1200903). This work is part of the ITI 2021–2028 program and supported by IdEx Unistra (ANR10-IDEX-0002 to E.W.), SFRI-STRAT’US project (ANR-20-SFRI-0012) and EUR IMCBio (IMCBio ANR-17-EURE-0023 to E.W.) under the framework of the French Investments for the Future Program. E.W. also acknowledges support from Wenzhou Institute, University of Chinese Academy of Sciences (WIUCASQD2024002). A.P. is supported by an NSF CAREER award CHE-2235785. M.A., M.P., J.S., T.Z. and M.S. are supported by the National Science Centre, Poland (2019/35/B/ST6/03074 to M.S.), the statutory funds of IBCH PAS and Poznan University of Technology. N.V.D. is supported by the National Institutes of Health (NIH) grants 1R35 GM134864 and the Passan Foundation. R.D. is supported by Stanford Bio-X (to R.D., R.O.D., R.C.K. and S.E.); Stanford Gerald J. Lieberman Fellowship (to R.R.); the NIH (R21 CA219847 and R35 GM122579 to R.D.), the Howard Hughes Medical Institute (to R.D.); Consejo Nacional de Ciencia y Tecnología CONACyT Fellowship 312765 (to P.C.); the Ruth L. Kirschstein National Research Service Award Postdoctoral Fellowships GM112294 (to J.D.Y.); National Science Foundation Graduate Research Fellowships (to R.J.L.T. and R.R.); the National Library of Medicine T15 Training Grant (NLM T15007033 to K.A.C.); and the US Department of Energy, Office of Science Graduate Student Research program (to R.J.L.T.). R.O.D. is supported by the US Department of Energy, Office of Science, Scientific Discovery through Advanced Computing (SciDAC) program and Intel. D.K. is supported by the NSF CAREER award MCB-2236996 and start-up, SURFF and START awards from the University of Maryland Baltimore County (to D.K.) and partly by the NIH T32 grant GM066706 (to N.K.D.). L.H. is supported by National Natural Science Foundation of China (32171191), Guangdong Science and Technology Department (2022A1515010328, 2023B1212060013 and 2020B1212030004) and Fundamental Research Funds for the Central Universities, Sun Yat-sen University (23ptpy41). J.Z. is supported by the Intramural Research Program of the NIH, the National Institute of Diabetes and Digestive and Kidney Diseases (ZIADK075136 to J.Z.), and an NIH Deputy Director for Intramural Research Challenge Award to J.Z. A.F.D. is supported, in part, by the intramural program of the National Heart, Lung and Blood Institute, NIH, USA. A.R. is supported by grants from the Natural Science Foundation of China (32325029, 32022039, 91940302 and 91640104) and the National Key Research and Development Project of China (2021YFC2300300 and 2023YFC2604300). C.N. and M.K. acknowledge funding from the National Science Centre. Poland (OPUS 2019/33/B/NZ2/02100). S.P.P. acknowledges funding from the National Science Centre, Poland (OPUS 2020/39/B/NZ2/01301). S.K. acknowledges funding from the National Science Centre, Poland (Sheng 2021/40/Q/NZ2/00078). C.N. acknowledges Polish high-performance computing infrastructure PLGrid (HPC Centers: PCSS, ACK Cyfronet AGH, CI TASK, WCSS) for providing computer facilities and support within the computational grants PLG/2022/016043, PLG/2022/015327 and PLG/2020/013424. J.Y. is supported in part by the National Natural Science Foundation of China (NSFC T2225007). B.M. is supported by the Interdisciplinary Thematic Institute IMCBio, as part of the ITI 2021-2028 program at the University of Strasbourg, CNRS and Inserm, by IdEx Unistra (ANR-10-IDEX-0002) and EUR (IMCBio ANR-17-EUR-0023), under the framework of the French Investments Program for the Future. R.T.B. is supported by a grant from the NIH (R01 GM073850). J.M.B. is supported by the National Science Centre in Poland (NCN grants 2017/26/A/NZ1/01083 to J.M.B., 2021/43/D/NZ1/03360 to S.M., 2020/39/B/NZ2/03127 to F.S. and 2020/39/D/NZ2/02837 to T.K.W.). E.F.B. was additionally supported by a European Molecular Biology Organization fellowship (ALTF 525-2022). J.M.B. acknowledges Poland high-performance computing infrastructure PLGrid (HPC Centers: ACK Cyfronet AGH, PCSS, CI TASK, WCSS) for providing computer facilities and support within the computational grant PLG/2023/016080. F.D. is supported by NIH R35GM145409 and P20GM121342. S.J.C. is supported by the NIH under grant R35-GM134919. J.W. is supported by the Penn State College of Medicine’s Artificial Intelligence and Biomedical Informatics Program. M.J.B. is supported by the Polish National Science Center Poland (grant 2016/23/B/ST6/03433). Predictions were performed using computational resources of the Interdisciplinary Centre for Mathematical and Computational Modelling of the University of Warsaw (grant G66-9). T.H.D.N. is supported by UKRI–Medical Research Council grant MC_UP_1201/19. S.P. is supported by the Fondecyt Regular project no. 1231071 and Centro Ciencia & Vida, FB210008, Financiamiento Basal para Centros Científicos y Tecnológicos de Excelencia de ANID. H.V.G. acknowledges financial support from the Ramón y Cajal grant no. RYC2022-038082-I and CEX2023-001263-S.
dc.description.urihttps://www.nature.com/articles/s41592-024-02543-9
dc.format.extent34 pages
dc.genrejournal articles
dc.identifierdoi:10.13016/m2oxyg-1kxd
dc.identifier.citationBu, Fan, Yagoub Adam, Ryszard W. Adamiak, Maciej Antczak, Belisa Rebeca H. de Aquino, Nagendar Goud Badepally, Robert T. Batey, et al. “RNA-Puzzles Round V: Blind Predictions of 23 RNA Structures.” Nature Methods, December 2, 2024, 1–13. https://doi.org/10.1038/s41592-024-02543-9.
dc.identifier.urihttps://doi.org/10.1038/s41592-024-02543-9
dc.identifier.urihttp://hdl.handle.net/11603/37718
dc.language.isoen_US
dc.publisherSpringer Nature
dc.relation.isAvailableAtThe University of Maryland, Baltimore County (UMBC)
dc.relation.ispartofUMBC Chemistry & Biochemistry Department
dc.relation.ispartofUMBC Staff Collection
dc.relation.ispartofUMBC Student Collection
dc.rightsThis work was written as part of one of the author's official duties as an Employee of the United States Government and is therefore a work of the United States Government. In accordance with 17 U.S.C. 105, no copyright protection is available for such works under U.S. Law.
dc.rightsPublic Domain
dc.rights.urihttps://creativecommons.org/publicdomain/mark/1.0/
dc.subjectStatistical methods
dc.subjectSoftware
dc.titleRNA-Puzzles Round V: blind predictions of 23 RNA structures
dc.typeText
dcterms.creatorhttps://orcid.org/0000-0001-6424-3173
dcterms.creatorhttps://orcid.org/0000-0002-5308-2746

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