ArticleNature methods2025
RNA-Puzzles Round V: blind predictions of 23 RNA structures.
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47 citing papers in PubMed.
- Molecular insights into dynamic RNA quaternary assemblies.RNA biology · 2026Review
- Hierarchical breakdown of RNA structure prediction in CASP16: from reliable local helices to speculative multimer assembly.Bioinformatics (Oxford, England) · 2026Article
- The trRosettaRNA server for RNA structure prediction.Nature protocols · 2026Review
- MERGE-RNA: a physics-based model to predict RNA secondary structure ensembles with chemical probing.Nucleic acids research · 2026Article
- Exploring Conformational Transitions of Adenine RNA Dimer via Machine Learning Potentials.Journal of chemical theory and computation · 2026Article
- Nearest Neighbor Parameters for Estimating RNA Folding Stability withbioRxiv : the preprint server for biology · 2026Article
- Limits of deep-learning-based RNA prediction methods.Nucleic acids research · 2026Article
- BRICHOS-Biased Inhibition Contributes to Aβ42 Dominance in Parenchymal Plaques Despite Higher Aβ40 Abundance and Coaggregation Capability.Biomacromolecules · 2026Article
- Bridging technical innovation and computational advances in studies of RNA-protein assemblies.Nature reviews. Genetics · 2026Review
- NuConf: a rotamer library for DNA and RNA and its implementation in the protein design software MUMBO.Scientific reports · 2026Article
- Identification of 3D motifs in Rfam with JAR3D.RNA (New York, N.Y.) · 2026Article
- R3J-AGNN: GNN-Based Prediction of Inter-Branch Angles in RNA Three-Way Junctions from Secondary Structure.Biology · 2026Article
- Article
- FRET-guided selection of RNA 3D structures.Nucleic acids research · 2026Article
- A retroelement-derived mammalian ARC protein exhibits selective RNA recognition and nucleic acid chaperone functions.Nucleic acids research · 2026Article
- Computational approaches for RNA structure prediction and design.Cell reports. Physical science · 2026Article
- Cat_Wiz: a stereochemistry-guided toolkit for locating, diagnosing, and annotating Mg2+ ions in RNA structures.Nucleic acids research · 2026Article
- gCoSRNA: Generalizable Coaxial Stacking Prediction for RNA Junctions Using Secondary Structure.Biomolecules · 2026Article
- DRfold2 is a deep learning-based tool that enables efficient and accurate RNA structure prediction.PLoS biology · 2026Article
- Integrated experimental and AI innovations for RNA structure determination.Nature biotechnology · 2026Review
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99 authors.
Fan BuGMU-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.
Yagoub AdamInter-institutional Graduate Program on Bioinformatics, Department of Computer Science and Mathematics, FFCLRP, University of São Paulo, Ribeirão Preto, Brazil.ORCID http://orcid.org/0000-0001-6874-2543
Ryszard W AdamiakInstitute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
Maciej AntczakInstitute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.ORCID http://orcid.org/0000-0002-5320-2023
Belisa Rebeca H de AquinoLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.
Nagendar Goud BadepallyLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.
Robert T BateyDepartment of Biochemistry, University of Colorado at Boulder, Boulder, CO, USA.ORCID http://orcid.org/0000-0002-1384-6625
Eugene F BaulinLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.ORCID http://orcid.org/0000-0003-4694-9783
Pawel BoinskiInstitute of Computing Science, Poznan University of Technology, Poznan, Poland.
Michal J BonieckiLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.
Janusz M BujnickiLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.ORCID http://orcid.org/0000-0002-6633-165X
Kristy A CarpenterDepartment of Biomedical Data Science, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0003-4570-5170
Jose ChaconDepartment of Biochemistry, Stanford University, Stanford, CA, USA.
Shi-Jie ChenDepartment of Physics, Department of Biochemistry and Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA.
Wah ChiuDepartment of Bioengineering and James H. Clark Center, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-8910-3078
Pablo CorderoDepartment of Biochemistry, Stanford University, Stanford, CA, USA.
Naba Krishna DasDepartment of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, USA.ORCID http://orcid.org/0000-0002-5308-2746
Rhiju DasDepartment of Biochemistry, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0001-7497-0972
Wayne K DawsonLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.ORCID http://orcid.org/0000-0001-7751-7778
Frank DiMaioDepartment of Biochemistry, University of Washington, Seattle, WA, USA.ORCID http://orcid.org/0000-0002-7524-8938
Feng DingDepartment of Physics and Astronomy, Clemson University, Clemson, SC, USA.ORCID http://orcid.org/0000-0003-1850-6336
Anne-Catherine Dock-BregeonLaboratory of Integrative Biology of Marine Models (LBI2M), Sorbonne University-CNRS UMR8227, Roscoff, France.
Nikolay V DokholyanDepartment of Pharmacology, Penn State College of Medicine, Hershey, PA, USA.ORCID http://orcid.org/0000-0002-8225-4025
Ron O DrorDepartment of Computer Science, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-6418-2793
Stanisław Dunin-HorkawiczLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.
Stephan EismannDepartment of Applied Physics, Stanford University, Stanford, CA, USA.
Eric EnnifarArchitecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, Strasbourg, France.
Reza EsmaeeliDepartment of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA.
Masoud Amiri FarsaniLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.
Adrian R Ferré-D'AmaréLaboratory of Nucleic Acids, National Heart, Lung and Blood Institute, Bethesda, MD, USA.ORCID http://orcid.org/0000-0003-4549-1619
Caleb GeniesseDepartment of Biochemistry, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-7897-8338
George E GhanimMedical Research Council Laboratory of Molecular Biology, Cambridge, UK.
Horacio V GuzmanInstituto de Ciencia de Materials de Barcelona, ICMAB-CSIC, Bellaterra E-08193, Spain & Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain.ORCID http://orcid.org/0000-0003-2564-3005
Iris V HoodLaboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA.
Lin HuangGuangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University Guangzhou, Guangdong, China.ORCID http://orcid.org/0000-0002-2121-365X
Dharm Skandh JainLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.
Farhang JaryaniLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.ORCID http://orcid.org/0000-0001-8374-6681
Lei JinDepartment of Physics, Department of Biochemistry and Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA.
Astha JoshiLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.ORCID http://orcid.org/0000-0003-4914-8228
Masha KarelinaBiophysics program, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0003-1880-4536
Jeffrey S KieftDepartment of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO, USA.
Wipapat KladwangDepartment of Biochemistry, Stanford University, Stanford, CA, USA.
Sebastian KmiecikLaboratory of Computational Biology, Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Warsaw, Poland.ORCID http://orcid.org/0000-0001-7623-0935
Deepak KoiralaDepartment of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, USA.ORCID http://orcid.org/0000-0001-6424-3173
Markus KollmannDepartment of Computer Science, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany.
Rachael C KretschBiophysics program, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-6935-518X
Mateusz KurcińskiLaboratory of Computational Biology, Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Warsaw, Poland.
Jun LiDepartment of Physics, Department of Biochemistry and Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA.ORCID http://orcid.org/0000-0002-7011-1991
Shuang LiLaboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA.
Marcin MagnusLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.ORCID http://orcid.org/0000-0002-5232-2234
BenoÎt MasquidaUMR 7156, CNRS - Université de Strasbourg, IPCB, Strasbourg, France.
S Naeim MoafinejadLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.ORCID http://orcid.org/0000-0003-0397-2596
Arup MondalDepartment of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA.
Sunandan MukherjeeLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.ORCID http://orcid.org/0000-0002-4361-0103
Thi Hoang Duong NguyenMedical Research Council Laboratory of Molecular Biology, Cambridge, UK.
Grigory NikolaevLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.ORCID http://orcid.org/0000-0002-5769-5400
Chandran NithinLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.ORCID http://orcid.org/0000-0001-8212-6093
Grace NyeHoward Hughes Medical Institute, Stanford University, Stanford, CA, USA.
Iswarya P N Pandaranadar JeyeramLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.ORCID http://orcid.org/0000-0002-4594-107X
Alberto PerezDepartment of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA.ORCID http://orcid.org/0000-0002-5054-5338
Phillip PhamHoward Hughes Medical Institute, Stanford University, Stanford, CA, USA.
Joseph A PiccirilliDepartment of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.ORCID http://orcid.org/0000-0002-0541-6270
Smita Priyadarshini PillaLaboratory of Computational Biology, Biological and Chemical Research Center, University of Warsaw, Warsaw, Poland.
Radosław PlutaLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.ORCID http://orcid.org/0000-0002-1676-860X
Simón PobleteFacultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile.
Almudena Ponce-SalvatierraLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.ORCID http://orcid.org/0000-0003-3966-8123
Mariusz PopendaInstitute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
Lukasz PopendaNanoBioMedical Centre, Adam Mickiewicz University, Poznan, Poland.ORCID http://orcid.org/0000-0003-1117-3081
Fabrizio PucciComputational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium.
Ramya RanganBiophysics program, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-0960-0825
Angana RayLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.
Aiming RenLife Sciences Institute, Zhejiang University, Hangzhou, China.ORCID http://orcid.org/0000-0002-5420-4899
Joanna SarzynskaInstitute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.ORCID http://orcid.org/0000-0002-0500-2238
Congzhou Mike ShaDepartment of Pharmacology, Penn State College of Medicine, Hershey, PA, USA.ORCID http://orcid.org/0000-0001-5301-9459
Filip StefaniakLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.ORCID http://orcid.org/0000-0001-5758-9416
Zhaoming SuThe State Key Laboratory of Biotherapy, West China Hospital, Chengdu, China.
Krishna C SuddalaLaboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA.ORCID http://orcid.org/0000-0003-1597-2622
Marta SzachniukInstitute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.ORCID http://orcid.org/0000-0002-8724-7908
Raphael TownshendDepartment of Computer Science, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0001-6362-1451
Robert J TrachmanLaboratory of Nucleic Acids, National Heart, Lung and Blood Institute, Bethesda, MD, USA.
Jian WangDepartment of Pharmacology, Penn State College of Medicine, Hershey, PA, USA.ORCID http://orcid.org/0000-0001-7768-2802
Wenkai WangMOE Frontiers Science Center for Nonlinear Expectations, Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao, China.ORCID http://orcid.org/0000-0001-8603-8250
Andrew WatkinsDepartment of Biochemistry, Stanford University, Stanford, CA, USA.
Tomasz K WireckiLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.
Yi XiaoSchool of Physics and Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan, China.ORCID http://orcid.org/0000-0001-8652-3651
Peng XiongSchool of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
Yiduo XiongSchool of Physics and Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan, China.
Jianyi YangMOE Frontiers Science Center for Nonlinear Expectations, Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao, China.ORCID http://orcid.org/0000-0003-2912-7737
Joseph David YesselmanHoward Hughes Medical Institute, Stanford University, Stanford, CA, USA.
Jinwei ZhangLaboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA.ORCID http://orcid.org/0000-0002-2114-173X
Yi ZhangSchool of Physics and Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan, China.
Zhenzhen ZhangDepartment of Physics and Astronomy, Clemson University, Clemson, SC, USA.
Yuanzhe ZhouDepartment of Physics, Department of Biochemistry and Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA.
Tomasz ZokInstitute of Computing Science, Poznan University of Technology, Poznan, Poland.ORCID http://orcid.org/0000-0003-4103-9238
Dong ZhangDepartment of Physics, Department of Biochemistry and Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA.
Sicheng ZhangDepartment of Physics, Department of Biochemistry and Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA.
Adriana ŻyłaLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.
Eric WesthofArchitecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, Strasbourg, France. e.westhof@ibmc-cnrs.unistra.fr.ORCID http://orcid.org/0000-0002-6172-5422
Zhichao MiaoGMU-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. miao_zhichao@gzlab.ac.cn.ORCID http://orcid.org/0000-0002-5777-9815
Funding
Tissue Structural and Neural Remodeling in Human Sacroiliac JointP20GM121342 · NIGMS · CLEMSON UNIVERSITY · PI Hai Yao · 2018 to 2026
$24.7MNoncoding RNA structures and interactions in cellular stress responses and immunityZIADK075136 · NIDDK · NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES · PI ZHANG, JINWEI · 2016 to 2025
$23.2MStructure, function, and dynamics of viral RNAs and RNA-containing complexesR35GM118070 · NIGMS · UNIVERSITY OF COLORADO DENVER · PI Jeffrey S Kieft · 2016 to 2026
$10.6MNext-generation computational/chemical methods for complex RNA structuresR35GM122579 · NIGMS · STANFORD UNIVERSITY · PI Rhiju Das · 2017 to 2026
$7.2MNanoscale programming of cellular and physiological phenotypes: EquipmentR35GM134864 · NIGMS · UNIVERSITY OF VIRGINIA · PI Nikolay Dokholyan · 2020 to 2026
$5.2MBasis of Gene Regulation by Purine-Binding mRNAsR01GM073850 · NIGMS · UNIVERSITY OF COLORADO AT BOULDER · PI BATEY, ROBERT T · 2005 to 2022
$4.8MMechanisms of viral RNA maturation by co-opting cellular exonucleasesR01AI133348 · NIAID · UNIVERSITY OF COLORADO DENVER · PI KIEFT, JEFFREY S · 2017 to 2025
$4.5MNew methods for computational modeling of RNA structuresR35GM134919 · NIGMS · UNIVERSITY OF MISSOURI-COLUMBIA · PI SHI-JIE CHEN · 2020 to 2026
$3.3MGraduate Training at The Chemistry Biology InterfaceT32GM066706 · NIGMS · UNIVERSITY OF MARYLAND BALTIMORE COUNTY · PI SELEY-RADTKE, KATHERINE L, SMITH, AARON T · 2004 to 2023
$3.3MInhibition of Human Islet Amyloid Polypeptide AggregationR35GM145409 · NIGMS · CLEMSON UNIVERSITY · PI Feng Ding · 2022 to 2026
$2.0MRiboswitches and their application to RNA visualization and transcription factor interactions with the transcriptomeR35GM152029 · NIGMS · UNIVERSITY OF COLORADO · PI Robert T Batey · 2024 to 2026
$1.8MComputational tools for understanding chemically modified RNA structure and interactionsR21CA219847 · NCI · STANFORD UNIVERSITY · PI DAS, RHIJU · 2017 to 2018
$334kFoundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.) P20GM121342Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.) R35GM145409Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.) T32 grant GM066706Intramural NIH HHS ZIA DK075136National Natural Science Foundation of China (National Science Foundation of China) 32171191National Natural Science Foundation of China (National Science Foundation of China) 32270707National Natural Science Foundation of China (National Science Foundation of China) NSFC T2225007NCI NIH HHS R21 CA219847NIAID NIH HHS R01 AI133348NIGMS NIH HHS F32 GM112294NIGMS NIH HHS P20 GM121342NIGMS NIH HHS R01 GM073850NIGMS NIH HHS R35 GM118070NIGMS NIH HHS R35 GM122579NIGMS NIH HHS R35 GM134864NIGMS NIH HHS R35 GM134919NIGMS NIH HHS R35 GM145409NIGMS NIH HHS T32 GM066706
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.
Indexed as
Computational BiologyNucleic Acid ConformationRNAAptamers, NucleotideModels, MolecularRNA, CatalyticAptamers, NucleotideRNARNA, Catalytic
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