ArticleRNA (New York, N.Y.)2017
RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme.
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Article in RNA (New York, N.Y.), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 126 papers.
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126 citing papers in PubMed, 204 citations in OpenAlex.
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- The RNA-Puzzles Assessments of RNA-Only Targets in CASP16.Proteins · 2026Article
- Interpretation of RNA Universe and Coding Potential Using IntRNA.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Predicting RNA Structure Utilizing Attention from Pretrained Language Models.Journal of chemical information and modeling · 2025Article
- Assessment of nucleic acid structure prediction in CASP16.bioRxiv : the preprint server for biology · 2025Article
- RNA-Puzzles Round V: blind predictions of 23 RNA structures.Nature methods · 2025Article
- NuFold: end-to-end approach for RNA tertiary structure prediction with flexible nucleobase center representation.Nature communications · 2025Article
- Transformers in RNA structure prediction: A review.Computational and structural biotechnology journal · 2025Review
- A virtual system-coupled molecular dynamics simulation free from experimental knowledge on binding sites: Application to RNA-ligand binding free-energy landscape.Biophysics and physicobiology · 2025Article
- RNA-TorsionBERT: leveraging language models for RNA 3D torsion angles prediction.Bioinformatics (Oxford, England) · 2024Article
- Accurate RNA 3D structure prediction using a language model-based deep learning approach.Nature methods · 2024Article
- Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction.PLoS computational biology · 2024Article
- RNAtango: Analysing and comparing RNA 3D structures via torsional angles.PLoS computational biology · 2024Article
66 more citing papers are in PubMed but not listed here.
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Authors and funding
46 authors at 15 institutions in 5 countries.
Zhichao MiaoArchitecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 67000 Strasbourg, France; z.miao@ibmc-cnrs.unistra.fr e.westhof@ibmc-cnrs.unistra.fr.ORCID 0000-0002-5777-9815
Ryszard W AdamiakInstitute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.ORCID 0000-0001-8914-9618
Maciej AntczakPoznan University of Technology, Institute of Computing Science, 60-965 Poznan, Poland.ORCID 0000-0002-5320-2023
Robert T BateyDepartment of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309-0596, USA.ORCID 0000-0001-8808-7646
Alexander J BeckaDepartment of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA.ORCID 0000-0002-1552-4881
Marcin BiesiadaInstitute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.
Michał J BonieckiLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland.
Janusz M BujnickiLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland.ORCID 0000-0002-6633-165X
Shi-Jie ChenDepartment of Physics and Astronomy, Department of Biochemistry, and Informatics Institute, University of Missouri-Columbia, Columbia, Missouri 65211, USA.ORCID 0000-0002-8093-7244
Clarence Yu ChengDepartment of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA.ORCID 0000-0003-3741-1906
Fang-Chieh ChouDepartment of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA.
Adrian R Ferré-D'AmaréNational Heart, Lung and Blood Institute, Bethesda, Maryland 20892-8012, USA.
Rhiju DasDepartment of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA.
Wayne K DawsonLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland.ORCID 0000-0003-3402-0774
Feng DingDepartment of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA.ORCID 0000-0001-5764-0963
Nikolay V DokholyanDepartment of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.ORCID 0000-0002-8225-4025
Stanisław Dunin-HorkawiczLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland.
Caleb GeniesseDepartment of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA.
Kalli KappelDepartment of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA.
Wipapat KladwangDepartment of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA.
Andrey KrokhotinDepartment of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.
Grzegorz E ŁachLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland.
François MajorInstitute for Research in Immunology and Cancer (IRIC), Department of Computer Science and Operations Research, Université de Montréal, Montréal, Québec, H3C 3J7, Canada.
Thomas H MannDepartment of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA.
Marcin MagnusDepartment of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA.ORCID 0000-0002-5232-2234
Katarzyna Pachulska-WieczorekInstitute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.
Dinshaw J PatelStructural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.
Joseph A PiccirilliDepartment of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA.
Mariusz PopendaInstitute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.
Katarzyna J PurzyckaInstitute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.
Aiming RenStructural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.
Greggory M RiceDepartment of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, USA.
John SantaluciaDepartment of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
Joanna SarzynskaInstitute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.ORCID 0000-0002-0500-2238
Marta SzachniukInstitute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.ORCID 0000-0002-0317-1820
Arpit TandonDepartment of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.
Jeremiah J TrauschDepartment of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309-0596, USA.
Siqi TianDepartment of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA.ORCID 0000-0001-5672-1032
Jian WangBiomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.
Kevin M WeeksDepartment of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, USA.
Benfeard WilliamsDepartment of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.
Yi XiaoBiomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.
Xiaojun XuDepartment of Physics and Astronomy, Department of Biochemistry, and Informatics Institute, University of Missouri-Columbia, Columbia, Missouri 65211, USA.ORCID 0000-0001-6811-9997
Dong ZhangDepartment of Physics and Astronomy, Department of Biochemistry, and Informatics Institute, University of Missouri-Columbia, Columbia, Missouri 65211, USA.
Tomasz ZokPoznan University of Technology, Institute of Computing Science, 60-965 Poznan, Poland.
Eric WesthofArchitecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 67000 Strasbourg, France; z.miao@ibmc-cnrs.unistra.fr e.westhof@ibmc-cnrs.unistra.fr.ORCID 0000-0002-6172-5422
Stanford University · USInstitute of Bioorganic Chemistry, Polish Academy of Sciences · PLInternational Institute of Molecular and Cell Biology · PLUniversity of North Carolina at Chapel Hill · USUniversity of Missouri · USCentre National de la Recherche Scientifique · FRHuazhong University of Science and Technology · CNMemorial Sloan Kettering Cancer Center · USPoznań University of Technology · PLUniversity of Colorado Boulder · USClemson University · USInstitute for Research in Immunology and Cancer · CANational Heart Lung and Blood Institute · USUniversity of Chicago · USWayne State University · US
Funding
Supplement to Enhance Wellness and Resiliency in the Graduate EnvironmentT32GM007276 · NIGMS · STANFORD UNIVERSITY · PI MORRISON, ASHBY J. · 1985 to 2023
$32.9MRNA: Structure, Biophysics and PhysiologyZIAHL006102 · NHLBI · NATIONAL HEART, LUNG, AND BLOOD INSTITUTE · PI FERRÉ-D'AMARÉ, ADRIAN · 2011 to 2025
$14.6MMolecular Biophysics Training Program at StanfordT32GM008294 · NIGMS · STANFORD UNIVERSITY · PI HUANG, KERWYN C. · 1989 to 2019
$7.4MBasis of Gene Regulation by Purine-Binding mRNAsR01GM073850 · NIGMS · UNIVERSITY OF COLORADO AT BOULDER · PI BATEY, ROBERT T · 2005 to 2022
$4.8MPredoctoral Training Program in Chemistry & BiologyT32GM008720 · NIGMS · UNIVERSITY OF CHICAGO · PI PICCIRILLI, JOSEPH ANTHONY · 1999 to 2020
$4.7MRetroviral Genomic RNA Dimer Structure and FunctionR01GM064803 · NIGMS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI WEEKS, KEVIN M · 2002 to 2016
$3.7MStatistical Mechanics of RNA FoldingR01GM063732 · NIGMS · UNIVERSITY OF MISSOURI-COLUMBIA · PI CHEN, SHI-JIE · 2003 to 2018
$3.2MCHAPERONE-ASSISTED RNA CRYSTALLOGRAPHY - Resubmission 01R01GM102489 · NIGMS · UNIVERSITY OF CHICAGO · PI PICCIRILLI, JOSEPH ANTHONY · 2013 to 2021
$2.9MStructure and Mechanism of SAM-responsive RiboswitchesR01GM083953 · NIGMS · UNIVERSITY OF COLORADO · PI BATEY, ROBERT T · 2008 to 2015
$2.4MInhibition of Human Islet Amyloid Polypeptide AggregationR35GM119691 · NIGMS · CLEMSON UNIVERSITY · PI DING, FENG · 2016 to 2020
$1.9MNon-coding RNA Structure through a Mutate-and-Map StrategyR01GM102519 · NIGMS · STANFORD UNIVERSITY · PI DAS, RHIJU · 2012 to 2016
$1.5MNIGMS NIH HHS R01 GM063732NIGMS NIH HHS R01 GM064803NIGMS NIH HHS R01 GM073850NIGMS NIH HHS R01 GM083953NIGMS NIH HHS R01 GM102489NIGMS NIH HHS R01 GM102519NIGMS NIH HHS R35 GM119691NIGMS NIH HHS T32 GM007276NIGMS NIH HHS T32 GM008294NIGMS NIH HHS T32 GM008720Wellcome Trust
Abstract
RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch aptamers and puzzle 7, a ribozyme structure, are included in this round of the experiment. The riboswitch structures include biological binding sites for small molecules (
Indexed as
RiboswitchAminoimidazole CarboxamideAptamers, NucleotideDinucleoside PhosphatesEndoribonucleasesGlutamineLigandsModels, MolecularNucleic Acid ConformationRibonucleotidesRNA, CatalyticS-Adenosylmethionine5-aminoimidazole-4-carboxamide-1-ribofuranosyl triphosphateAminoimidazole CarboxamideAptamers, Nucleotidecyclic diadenosine phosphateDinucleoside PhosphatesEndoribonucleasesGlutamineLigandsRibonucleotidesRiboswitchRNA, CatalyticS-Adenosylmethioninevarkud satellite ribozyme3D predictionbioinformaticsforce fieldsmodelsstructure qualityX-ray structures
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