ArticleRNA (New York, N.Y.)2020
RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers.
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Article in RNA (New York, N.Y.), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 106 papers.
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106citing papers in PubMed
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Who cites it
106 citing papers in PubMed.
- Crosstalk between RNA secondary and three-dimensional structure prediction: a comprehensive study.RNA biology · 2026Article
- Nearest Neighbor Parameters for Estimating RNA Folding Stability withbioRxiv : the preprint server for biology · 2026Article
- RNAbpFlow: base pair-augmented SE(3) flow matching for conditional RNA 3D structure generation.Nature methods · 2026Article
- Open questions on viral frameshifting: Exploiting the structural plasticity of the frameshifting element for therapeutic intervention.Biophysical journal · 2026Review
- Spectral Graph Features for Reference-free RNA 3D Quality Assessment.bioRxiv : the preprint server for biology · 2026Article
- FRET-guided selection of RNA 3D structures.Nucleic acids research · 2026Article
- Computational approaches for RNA structure prediction and design.Cell reports. Physical science · 2026Article
- Harnessing deep learning to accelerate the development of antibodies and aptamers.Acta pharmaceutica Sinica. B · 2026Review
- TiRNA: a coarse-grained method with temperature and ion effects for RNA structure folding and prediction.Nucleic acids research · 2026Article
- Decoding RNA triple helices: identification from sequence and secondary structure.Briefings in bioinformatics · 2026Article
- Assessment of Nucleic Acid Structure Prediction in CASP16.Proteins · 2026Article
- Structure Modeling Protocols for Protein Multimer and RNA in CASP16 With Enhanced MSAs, Model Ranking, and Deep Learning.Proteins · 2026Article
- The RNA-Puzzles Assessments of RNA-Only Targets in CASP16.Proteins · 2026Article
- Enhancing RNA 3D Structure Prediction in CASP16: Integrating Physics-Based Modeling With Machine Learning for Improved Predictions.Proteins · 2026Article
- PARSEbp: pairwise agreement-based RNA scoring with emphasis on base pairings.Bioinformatics advances · 2026Article
- Artificial intelligence in bioinformatics: a survey.Briefings in bioinformatics · 2025Review
- PARSEbp: Pairwise Agreement-based RNA Scoring with Emphasis on Base Pairings.bioRxiv : the preprint server for biology · 2025Article
- Can geometric combinatorics improve RNA branching predictions?BMC bioinformatics · 2025Article
- RNAbpFlow: Base pair-augmented SE(3)-flow matching for conditional RNA 3D structure generation.bioRxiv : the preprint server for biology · 2025Article
- rsRNASP1: A distance- and dihedral-dependent statistical potential for RNA 3D structure evaluation.Biophysical journal · 2025Article
46 more citing papers are in PubMed but not listed here.
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Authors and funding
50 authors.
Zhichao MiaoTranslational Research Institute of Brain and Brain-Like Intelligence and Department of Anesthesiology, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai 200081, China.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 AntczakInstitute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.ORCID 0000-0002-5320-2023
Michał J BonieckiInternational Institute of Molecular and Cell Biology in Warsaw, Księcia Trojdena 4, 02-109 Warsaw, Poland.ORCID 0000-0002-8010-0751
Janusz BujnickiInternational Institute of Molecular and Cell Biology in Warsaw, Księcia Trojdena 4, 02-109 Warsaw, Poland.ORCID 0000-0002-6633-165X
Shi-Jie ChenDepartment of Physics and Astronomy, Department of Biochemistry, MU Institute for Data Science and Informatics, University of Missouri-Columbia, Missouri 65211, USA.
Clarence Yu ChengDepartment of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA.ORCID 0000-0003-3741-1906
Yi ChengDepartment of Physics and Astronomy, Department of Biochemistry, MU Institute for Data Science and Informatics, University of Missouri-Columbia, Missouri 65211, USA.
Fang-Chieh ChouDepartment of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA.
Rhiju DasDepartment of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA.ORCID 0000-0001-7497-0972
Nikolay V DokholyanDepartment of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania, 17033, USA.ORCID 0000-0002-8225-4025
Feng DingDepartment of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA.
Caleb GeniesseDepartment of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA.ORCID 0000-0002-7897-8338
Yangwei JiangDepartment of Physics and Astronomy, Department of Biochemistry, MU Institute for Data Science and Informatics, University of Missouri-Columbia, Missouri 65211, USA.
Astha JoshiInternational Institute of Molecular and Cell Biology in Warsaw, Księcia Trojdena 4, 02-109 Warsaw, Poland.ORCID 0000-0003-4914-8228
Andrey KrokhotinDepartment of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.
Marcin MagnusInternational Institute of Molecular and Cell Biology in Warsaw, Księcia Trojdena 4, 02-109 Warsaw, Poland.ORCID 0000-0002-5232-2234
Olivier MailhotInstitute for Research in Immunology and Cancer (IRIC), Department of Computer Science and Operations Research, Université de Montréal, Montréal, Québec, H3C 3J7, Canada.
Francois MajorInstitute for Research in Immunology and Cancer (IRIC), Department of Computer Science and Operations Research, Université de Montréal, Montréal, Québec, H3C 3J7, Canada.ORCID 0000-0003-1743-0480
Thomas H MannDepartment of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA.
Paweł PiątkowskiInternational Institute of Molecular and Cell Biology in Warsaw, Księcia Trojdena 4, 02-109 Warsaw, Poland.
Radoslaw PlutaInternational Institute of Molecular and Cell Biology in Warsaw, Księcia Trojdena 4, 02-109 Warsaw, Poland.ORCID 0000-0002-1676-860X
Mariusz PopendaInstitute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.ORCID 0000-0001-9965-0430
Joanna SarzynskaInstitute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.ORCID 0000-0002-0500-2238
Lizhen SunDepartment of Physics and Astronomy, Department of Biochemistry, MU Institute for Data Science and Informatics, University of Missouri-Columbia, Missouri 65211, USA.
Marta SzachniukInstitute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.ORCID 0000-0002-8724-7908
Siqi TianDepartment of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA.
Jian WangDepartment of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania, 17033, USA.
Jun WangSchool of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.
Andrew M WatkinsDepartment of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA.ORCID 0000-0003-1617-1720
Jakub WiedemannInstitute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.ORCID 0000-0003-0138-5988
Yi XiaoSchool of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.
Xiaojun XuDepartment of Physics and Astronomy, Department of Biochemistry, MU Institute for Data Science and Informatics, University of Missouri-Columbia, Missouri 65211, USA.
Joseph D YesselmanDepartment of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA.
Dong ZhangDepartment of Physics and Astronomy, Department of Biochemistry, MU Institute for Data Science and Informatics, University of Missouri-Columbia, Missouri 65211, USA.
Yi ZhangSchool of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.
Zhenzhen ZhangDepartment of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA.
Chenhan ZhaoDepartment of Physics and Astronomy, Department of Biochemistry, MU Institute for Data Science and Informatics, University of Missouri-Columbia, Missouri 65211, USA.
Peinan ZhaoDepartment of Physics and Astronomy, Department of Biochemistry, MU Institute for Data Science and Informatics, University of Missouri-Columbia, Missouri 65211, USA.
Yuanzhe ZhouDepartment of Physics and Astronomy, Department of Biochemistry, MU Institute for Data Science and Informatics, University of Missouri-Columbia, Missouri 65211, USA.
Tomasz ZokInstitute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland.
Adriana ŻyłaInternational Institute of Molecular and Cell Biology in Warsaw, Księcia Trojdena 4, 02-109 Warsaw, Poland.ORCID 0000-0002-5109-0208
Aiming RenLife Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China.ORCID 0000-0002-5420-4899
Robert T BateyDepartment of Biochemistry, University of Colorado at Boulder, Campus Box 596, Boulder, Colorado 80309-0596, USA.ORCID 0000-0002-1384-6625
Barbara L GoldenDepartment of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA.ORCID 0000-0002-9741-882X
Lin HuangGuangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, P. R. China.ORCID 0000-0002-2121-365X
David M LilleyCancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom.ORCID 0000-0001-6882-2818
Yijin LiuCancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom.ORCID 0000-0002-3643-8683
Dinshaw J PatelStructural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.ORCID 0000-0002-9779-7778
Eric WesthofArch et Reactivite de l'ARN, Univ de Strasbourg, Inst de Biol Mol et Cell du CNRS, 67084 Strasbourg, France.
Funding
X-RAY CRYSTALLOGRAPHYP30CA008748 · NCI · SLOAN-KETTERING INSTITUTE FOR CANCER RES · PI Hongbiao Carl Lekaye · 1985 to 2026
$347.4MPenn State Clinical and Translational Science InstituteUL1TR002014 · NCATS · PENNSYLVANIA STATE UNIV HERSHEY MED CTR · PI KRASCHNEWSKI, JENNIFER L. · 2016 to 2025
$33.7MNext-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
$4.8MNew methods for computational modeling of RNA structuresR35GM134919 · NIGMS · UNIVERSITY OF MISSOURI-COLUMBIA · PI SHI-JIE CHEN · 2020 to 2026
$3.3MStatistical Mechanics of RNA FoldingR01GM063732 · NIGMS · UNIVERSITY OF MISSOURI-COLUMBIA · PI CHEN, SHI-JIE · 2003 to 2018
$3.2MEngineering allostery for in vivo protein controlR01GM123247 · NIGMS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI DOKHOLYAN, NIKOLAY · 2017 to 2019
$1.5MNew computational tools for predicting ion effects in RNA structuresR01GM117059 · NIGMS · UNIVERSITY OF MISSOURI-COLUMBIA · PI CHEN, SHI-JIE · 2017 to 2020
$1.2MIntegrating cheminformatics and molecular simulations for virtual drug screeningR01GM114015 · NIGMS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI DOKHOLYAN, NIKOLAY · 2016 to 2019
$1.1MComputational tools for understanding chemically modified RNA structure and interactionsR21CA219847 · NCI · STANFORD UNIVERSITY · PI DAS, RHIJU · 2017 to 2018
$334kCorrecting Pervasive Errors in RNA Crystallography with RosettaR21GM102716 · NIGMS · STANFORD UNIVERSITY · PI DAS, RHIJU · 2012 to 2013
$302kNCATS NIH HHS UL1 TR002014NCI NIH HHS P30 CA008748NCI NIH HHS R21 CA219847NIGMS NIH HHS R01 GM063732NIGMS NIH HHS R01 GM073850NIGMS NIH HHS R01 GM114015NIGMS NIH HHS R01 GM117059NIGMS NIH HHS R01 GM123247NIGMS NIH HHS R21 GM102716NIGMS NIH HHS R35 GM122579NIGMS NIH HHS R35 GM134864NIGMS NIH HHS R35 GM134919Wellcome Trust
Abstract
RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA 3D structure prediction. With agreement from crystallographers, the RNA structures are predicted by various groups before the publication of the crystal structures. We now report the prediction of 3D structures for six RNA sequences: four nucleolytic ribozymes and two riboswitches. Systematic protocols for comparing models and crystal structures are described and analyzed. In these six puzzles, we discuss (i) the comparison between the automated web servers and human experts; (ii) the prediction of coaxial stacking; (iii) the prediction of structural details and ligand binding; (iv) the development of novel prediction methods; and (v) the potential improvements to be made. We show that correct prediction of coaxial stacking and tertiary contacts is essential for the prediction of RNA architecture, while ligand binding modes can only be predicted with low resolution and simultaneous prediction of RNA structure with accurate ligand binding still remains out of reach. All the predicted models are available for the future development of force field parameters and the improvement of comparison and assessment tools.
Indexed as
Aptamers, NucleotideBase SequenceLigandsNucleic Acid ConformationRiboswitchRNARNA, CatalyticAptamers, NucleotideLigandsRiboswitchRNARNA, CatalyticaptamermodelingpredictionribozymeRNA structure
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