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

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

doi:10.1038/s41592-024-02543-9

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

Journal Article · 02 December 2024 · Nature Methods

DOI: https://doi.org/10.1038/s41592-024-02543-9 · OSTI ID:2497760

Bu, Fan ^[1];

; Adamiak, Ryszard W.;

; de Aquino, Belisa H.; Badepally, Nagendar Goud;

;

; Boinski, Pawel; Boniecki, Michal J.;

;

; Chacon, Jose; Chen, Shi-Jie;

; Cordero, Pablo;

;

Guangzhou National Laboratory (China); Guangzhou Medical University (China); University of Science and Technology of China, Hefei (China); et al.
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Advanced Scientific Computing Research (ASCR). Scientific Discovery through Advanced Computing (SciDAC); USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science (BSS)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2497760

Journal Information:: Nature Methods, Journal Name: Nature Methods Vol. 22; ISSN 1548-7091

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

References (135)

Deriving effective mesoscale potentials from atomistic simulations: Mesoscale Potentials from Atomistic Simulations Reith, Dirk; Pütz, Mathias; Müller-Plathe, Florian Journal of Computational Chemistry, Vol. 24, Issue 13 https://doi.org/10.1002/jcc.10307	journal	August 2003
UCSF Chimera?A visualization system for exploratory research and analysis Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C. Journal of Computational Chemistry, Vol. 25, Issue 13 https://doi.org/10.1002/jcc.20084	journal	January 2004
MolProbity: More and better reference data for improved all-atom structure validation: PROTEIN SCIENCE.ORG Williams, Christopher J.; Headd, Jeffrey J.; Moriarty, Nigel W. Protein Science, Vol. 27, Issue 1 https://doi.org/10.1002/pro.3330	journal	November 2017
RNA target highlights in CASP15: Evaluation of predicted models by structure providers Kretsch, Rachael C.; Andersen, Ebbe S.; Bujnicki, Janusz M. Proteins: Structure, Function, and Bioinformatics, Vol. 91, Issue 12 https://doi.org/10.1002/prot.26550	journal	July 2023
RNA tertiary structure modeling with BRiQ potential in CASP15 Chen, Ke; Zhou, Yaoqi; Wang, Sheng Proteins: Structure, Function, and Bioinformatics, Vol. 91, Issue 12 https://doi.org/10.1002/prot.26574	journal	August 2023
RNA tertiary structure prediction using RNAComposer in CASP15 Sarzynska, Joanna; Popenda, Mariusz; Antczak, Maciej Proteins: Structure, Function, and Bioinformatics, Vol. 91, Issue 12 https://doi.org/10.1002/prot.26578	journal	August 2023
Advancing RNA 3D structure prediction: Exploring hierarchical and hybrid approaches in CASP15 Li, Jun; Zhang, Sicheng; Chen, Shi‐Jie Proteins: Structure, Function, and Bioinformatics, Vol. 91, Issue 12 https://doi.org/10.1002/prot.26583	journal	August 2023
Assessment of three‐dimensional RNA structure prediction in CASP15 Das, Rhiju; Kretsch, Rachael C.; Simpkin, Adam J. Proteins: Structure, Function, and Bioinformatics, Vol. 91, Issue 12 https://doi.org/10.1002/prot.26602	journal	October 2023
CASP15 cryo‐EM protein and RNA targets: Refinement and analysis using experimental maps Mulvaney, Thomas; Kretsch, Rachael C.; Elliott, Luc Proteins: Structure, Function, and Bioinformatics, Vol. 91, Issue 12 https://doi.org/10.1002/prot.26644	journal	November 2023
An overview of the Amber biomolecular simulation package: Amber biomolecular simulation package Salomon-Ferrer, Romelia; Case, David A.; Walker, Ross C. Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 3, Issue 2 https://doi.org/10.1002/wcms.1121	journal	September 2012
Discrete molecular dynamics: Discrete Molecular Dynamics Proctor, Elizabeth A.; Ding, Feng; Dokholyan, Nikolay V. Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 1, Issue 1 https://doi.org/10.1002/wcms.4	journal	January 2011
The two faces of the Escherichia coli 23 S rRNA sarcin/ricin domain: the structure at 1.11 Å resolution 1 1Edited by D. E. Draper Correll, Carl C.; Wool, Ira G.; Munishkin, Alexander Journal of Molecular Biology, Vol. 292, Issue 2 https://doi.org/10.1006/jmbi.1999.3072	journal	September 1999
Quantitative analysis of nucleic acid three-dimensional structures Gendron, Patrick; Lemieux, Sébastien; Major, François Journal of Molecular Biology, Vol. 308, Issue 5 https://doi.org/10.1006/jmbi.2001.4626	journal	May 2001
Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis Michel, François; Westhof, Eric Journal of Molecular Biology, Vol. 216, Issue 3 https://doi.org/10.1016/0022-2836(90)90386-Z	journal	December 1990
Rosetta3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules Leaver-Fay, Andrew; Tyka, Michael; Lewis, Steven M. Computer Methods, Part C https://doi.org/10.1016/B978-0-12-381270-4.00019-6	book	January 2011
Replica-exchange molecular dynamics method for protein folding Sugita, Yuji; Okamoto, Yuko Chemical Physics Letters, Vol. 314, Issue 1-2 https://doi.org/10.1016/S0009-2614(99)01123-9	journal	November 1999
Predicting 3D RNA structure from solely the nucleotide sequence using Euclidean distance neural networks Sha, Congzhou M.; Wang, Jian; Dokholyan, Nikolay V. Biophysical Journal, Vol. 122, Issue 3 https://doi.org/10.1016/j.bpj.2022.11.2396	journal	February 2023
Predicting 3D RNA structure from the nucleotide sequence using Euclidean neural networks Sha, Congzhou M.; Wang, Jian; Dokholyan, Nikolay V. Biophysical Journal, Vol. 123, Issue 17 https://doi.org/10.1016/j.bpj.2023.10.011	journal	September 2024
SPFP: Speed without compromise—A mixed precision model for GPU accelerated molecular dynamics simulations Le Grand, Scott; Götz, Andreas W.; Walker, Ross C. Computer Physics Communications, Vol. 184, Issue 2 https://doi.org/10.1016/j.cpc.2012.09.022	journal	February 2013
3dRNA: Building RNA 3D structure with improved template library Zhang, Yi; Wang, Jun; Xiao, Yi Computational and Structural Biotechnology Journal, Vol. 18 https://doi.org/10.1016/j.csbj.2020.08.017	journal	January 2020
rMSA: A Sequence Search and Alignment Algorithm to Improve RNA Structure Modeling Zhang, Chengxin; Zhang, Yang; Pyle, Anna Marie Journal of Molecular Biology, Vol. 435, Issue 14 https://doi.org/10.1016/j.jmb.2022.167904	journal	July 2023
VfoldLA: A web server for loop assembly-based prediction of putative 3D RNA structures Xu, Xiaojun; Zhao, Chenhan; Chen, Shi-Jie Journal of Structural Biology, Vol. 207, Issue 3 https://doi.org/10.1016/j.jsb.2019.06.002	journal	September 2019
FARFAR2: Improved De Novo Rosetta Prediction of Complex Global RNA Folds Watkins, Andrew Martin; Rangan, Ramya; Das, Rhiju Structure, Vol. 28, Issue 8 https://doi.org/10.1016/j.str.2020.05.011	journal	August 2020
Geometric nomenclature and classification of RNA base pairs Leontis, Neocles B.; Westhof, Eric RNA, Vol. 7, Issue 4 https://doi.org/10.1017/S1355838201002515	journal	April 2001
IsRNA1: De Novo Prediction and Blind Screening of RNA 3D Structures Zhang, Dong; Li, Jun; Chen, Shi-Jie Journal of Chemical Theory and Computation, Vol. 17, Issue 3 https://doi.org/10.1021/acs.jctc.0c01148	journal	February 2021
Refinement of Generalized Born Implicit Solvation Parameters for Nucleic Acids and Their Complexes with Proteins Nguyen, Hai; Pérez, Alberto; Bermeo, Sherry Journal of Chemical Theory and Computation, Vol. 11, Issue 8 https://doi.org/10.1021/acs.jctc.5b00271	journal	July 2015
IsRNA: An Iterative Simulated Reference State Approach to Modeling Correlated Interactions in RNA Folding Zhang, Dong; Chen, Shi-Jie Journal of Chemical Theory and Computation, Vol. 14, Issue 4 https://doi.org/10.1021/acs.jctc.7b01228	journal	March 2018
Vfold2D-MC: A Physics-Based Hybrid Model for Predicting RNA Secondary Structure Folding Cheng, Yi; Zhang, Sicheng; Xu, Xiaojun The Journal of Physical Chemistry B, Vol. 125, Issue 36 https://doi.org/10.1021/acs.jpcb.1c04731	journal	September 2021
The SARS-CoV-2 Programmed −1 Ribosomal Frameshifting Element Crystal Structure Solved to 2.09 Å Using Chaperone-Assisted RNA Crystallography Roman, Christina; Lewicka, Anna; Koirala, Deepak ACS Chemical Biology, Vol. 16, Issue 8 https://doi.org/10.1021/acschembio.1c00324	journal	July 2021
Quantitative Dimethyl Sulfate Mapping for Automated RNA Secondary Structure Inference Cordero, Pablo; Kladwang, Wipapat; VanLang, Christopher C. Biochemistry, Vol. 51, Issue 36 https://doi.org/10.1021/bi3008802	journal	August 2012
Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins Banáš, Pavel; Hollas, Daniel; Zgarbová, Marie Journal of Chemical Theory and Computation, Vol. 6, Issue 12 https://doi.org/10.1021/ct100481h	journal	November 2010
Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles Zgarbová, Marie; Otyepka, Michal; Šponer, Jiří Journal of Chemical Theory and Computation, Vol. 7, Issue 9 https://doi.org/10.1021/ct200162x	journal	August 2011
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born Götz, Andreas W.; Williamson, Mark J.; Xu, Dong Journal of Chemical Theory and Computation, Vol. 8, Issue 5 https://doi.org/10.1021/ct200909j	journal	April 2012
Improved Generalized Born Solvent Model Parameters for Protein Simulations Nguyen, Hai; Roe, Daniel R.; Simmerling, Carlos Journal of Chemical Theory and Computation, Vol. 9, Issue 4 https://doi.org/10.1021/ct3010485	journal	March 2013
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald Salomon-Ferrer, Romelia; Götz, Andreas W.; Poole, Duncan Journal of Chemical Theory and Computation, Vol. 9, Issue 9 https://doi.org/10.1021/ct400314y	journal	August 2013
Physics-Based De Novo Prediction of RNA 3D Structures Cao, Song; Chen, Shi-Jie The Journal of Physical Chemistry B, Vol. 115, Issue 14 https://doi.org/10.1021/jp112059y	journal	April 2011
Atomic accuracy in predicting and designing noncanonical RNA structure Das, Rhiju; Karanicolas, John; Baker, David Nature Methods, Vol. 7, Issue 4 https://doi.org/10.1038/nmeth.1433	journal	February 2010
Parmbsc1: a refined force field for DNA simulations Ivani, Ivan; Dans, Pablo D.; Noy, Agnes Nature Methods, Vol. 13, Issue 1 https://doi.org/10.1038/nmeth.3658	journal	November 2015
Crystal structure of an adenovirus virus-associated RNA Hood, Iris V.; Gordon, Jackson M.; Bou-Nader, Charles Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-10752-6	journal	June 2019
RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning Singh, Jaswinder; Hanson, Jack; Paliwal, Kuldip Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-13395-9	journal	November 2019
Crystal structure of a highly conserved enteroviral 5′ cloverleaf RNA replication element Das, Naba K.; Hollmann, Nele M.; Vogt, Jeff Nature Communications, Vol. 14, Issue 1 https://doi.org/10.1038/s41467-023-37658-8	journal	April 2023
trRosettaRNA: automated prediction of RNA 3D structure with transformer network Wang, Wenkai; Feng, Chenjie; Han, Renmin Nature Communications, Vol. 14, Issue 1 https://doi.org/10.1038/s41467-023-42528-4	journal	November 2023
Structure of human telomerase holoenzyme with bound telomeric DNA Ghanim, George E.; Fountain, Adam J.; van Roon, Anne-Marie M. Nature, Vol. 593, Issue 7859 https://doi.org/10.1038/s41586-021-03415-4	journal	April 2021
Structure and functional reselection of the Mango-III fluorogenic RNA aptamer Trachman, Robert J.; Autour, Alexis; Jeng, Sunny C. Y. Nature Chemical Biology, Vol. 15, Issue 5 https://doi.org/10.1038/s41589-019-0267-9	journal	April 2019
Structure-based investigation of fluorogenic Pepper aptamer Huang, Kaiyi; Chen, Xianjun; Li, Chunyan Nature Chemical Biology, Vol. 17, Issue 12 https://doi.org/10.1038/s41589-021-00884-6	journal	November 2021
Structure and mechanism of a methyltransferase ribozyme Deng, Jie; Wilson, Timothy J.; Wang, Jia Nature Chemical Biology, Vol. 18, Issue 5 https://doi.org/10.1038/s41589-022-00982-z	journal	March 2022
Cryo-EM and antisense targeting of the 28-kDa frameshift stimulation element from the SARS-CoV-2 RNA genome Zhang, Kaiming; Zheludev, Ivan N.; Hagey, Rachel J. Nature Structural & Molecular Biology, Vol. 28, Issue 9 https://doi.org/10.1038/s41594-021-00653-y	journal	August 2021
Automated and fast building of three-dimensional RNA structures Zhao, Yunjie; Huang, Yangyu; Gong, Zhou Scientific Reports, Vol. 2, Issue 1 https://doi.org/10.1038/srep00734	journal	October 2012
Comparison of simple potential functions for simulating liquid water Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D. The Journal of Chemical Physics, Vol. 79, Issue 2 https://doi.org/10.1063/1.445869	journal	July 1983
A smooth particle mesh Ewald method Essmann, Ulrich; Perera, Lalith; Berkowitz, Max L. The Journal of Chemical Physics, Vol. 103, Issue 19 https://doi.org/10.1063/1.470117	journal	November 1995
Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference MacCallum, Justin L.; Perez, Alberto; Dill, Ken A. Proceedings of the National Academy of Sciences, Vol. 112, Issue 22 https://doi.org/10.1073/pnas.1506788112	journal	May 2015
Accelerating molecular simulations of proteins using Bayesian inference on weak information Perez, Alberto; MacCallum, Justin L.; Dill, Ken A. Proceedings of the National Academy of Sciences, Vol. 112, Issue 38 https://doi.org/10.1073/pnas.1515561112	journal	September 2015
Hatchet ribozyme structure and implications for cleavage mechanism Zheng, Luqian; Falschlunger, Christoph; Huang, Kaiyi Proceedings of the National Academy of Sciences, Vol. 116, Issue 22 https://doi.org/10.1073/pnas.1902413116	journal	May 2019
A Modified Version of the Cornell et al. Force Field with Improved Sugar Pucker Phases and Helical Repeat Cheatham, Thomas E.; Cieplak, Piotr; Kollman, Peter A. Journal of Biomolecular Structure and Dynamics, Vol. 16, Issue 4 https://doi.org/10.1080/07391102.1999.10508297	journal	February 1999
RNAloops: a database of RNA multiloops Wiedemann, Jakub; Kaczor, Jacek; Milostan, Maciej Bioinformatics, Vol. 38, Issue 17 https://doi.org/10.1093/bioinformatics/btac484	journal	July 2022
CONTRAfold: RNA secondary structure prediction without physics-based models Do, C. B.; Woods, D. A.; Batzoglou, S. Bioinformatics, Vol. 22, Issue 14 https://doi.org/10.1093/bioinformatics/btl246	journal	July 2006
iFoldRNA: three-dimensional RNA structure prediction and folding Sharma, Shantanu; Ding, Feng; Dokholyan, Nikolay V. Bioinformatics, Vol. 24, Issue 17 https://doi.org/10.1093/bioinformatics/btn328	journal	June 2008
PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta Chaudhury, S.; Lyskov, S.; Gray, J. J. Bioinformatics, Vol. 26, Issue 5, p. 689-691 https://doi.org/10.1093/bioinformatics/btq007	journal	January 2010
IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming Sato, Kengo; Kato, Yuki; Hamada, Michiaki Bioinformatics, Vol. 27, Issue 13 https://doi.org/10.1093/bioinformatics/btr215	journal	June 2011
lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests Mariani, Valerio; Biasini, Marco; Barbato, Alessandro Bioinformatics, Vol. 29, Issue 21 https://doi.org/10.1093/bioinformatics/btt473	journal	August 2013
Infernal 1.1: 100-fold faster RNA homology searches Nawrocki, E. P.; Eddy, S. R. Bioinformatics, Vol. 29, Issue 22 https://doi.org/10.1093/bioinformatics/btt509	journal	September 2013
The RNA shapes studio Janssen, Stefan; Giegerich, Robert Bioinformatics, Vol. 31, Issue 3 https://doi.org/10.1093/bioinformatics/btu649	journal	October 2014
iFoldRNA v2: folding RNA with constraints Krokhotin, Andrey; Houlihan, Kevin; Dokholyan, Nikolay V. Bioinformatics, Vol. 31, Issue 17 https://doi.org/10.1093/bioinformatics/btv221	journal	April 2015
Primerize-2D: automated primer design for RNA multidimensional chemical mapping Tian, Siqi; Das, Rhiju Bioinformatics, Vol. 33, Issue 9 https://doi.org/10.1093/bioinformatics/btw814	journal	January 2017
New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation Antczak, Maciej; Popenda, Mariusz; Zok, Tomasz Bioinformatics, Vol. 34, Issue 8 https://doi.org/10.1093/bioinformatics/btx783	journal	December 2017
RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA Gong, Sha; Zhang, Chengxin; Zhang, Yang Bioinformatics, Vol. 35, Issue 21 https://doi.org/10.1093/bioinformatics/btz282	journal	April 2019
pydca v1.0: a comprehensive software for direct coupling analysis of RNA and protein sequences Zerihun, Mehari B.; Pucci, Fabrizio; Peter, Emanuel K. Bioinformatics, Vol. 36, Issue 7 https://doi.org/10.1093/bioinformatics/btz892	journal	November 2019
The Protein Data Bank Berman, H. M. Nucleic Acids Research, Vol. 28, Issue 1 https://doi.org/10.1093/nar/28.1.235	journal	January 2000
Rfam 14: expanded coverage of metagenomic, viral and microRNA families Kalvari, Ioanna; Nawrocki, Eric P.; Ontiveros-Palacios, Nancy Nucleic Acids Research, Vol. 49, Issue D1 https://doi.org/10.1093/nar/gkaa1047	journal	November 2020
RNAProbe: a web server for normalization and analysis of RNA structure probing data Wirecki, Tomasz K.; Merdas, Katarzyna; Bernat, Agata Nucleic Acids Research, Vol. 48, Issue W1 https://doi.org/10.1093/nar/gkaa396	journal	June 2020
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases Nucleic Acids Research, Vol. 49, Issue D1, p. D212-D220 https://doi.org/10.1093/nar/gkaa921	journal	October 2020
Database resources of the national center for biotechnology information Sayers, Eric W.; Bolton, Evan E.; Brister, J. Rodney Nucleic Acids Research, Vol. 50, Issue D1 https://doi.org/10.1093/nar/gkab1112	journal	December 2021
ONQUADRO: a database of experimentally determined quadruplex structures Zok, Tomasz; Kraszewska, Natalia; Miskiewicz, Joanna Nucleic Acids Research, Vol. 50, Issue D1 https://doi.org/10.1093/nar/gkab1118	journal	November 2021
Insights into xanthine riboswitch structure and metal ion-mediated ligand recognition Xu, Xiaochen; Egger, Michaela; Chen, Hao Nucleic Acids Research, Vol. 49, Issue 12 https://doi.org/10.1093/nar/gkab486	journal	June 2021
Entanglements of structure elements revealed in RNA 3D models Popenda, Mariusz; Zok, Tomasz; Sarzynska, Joanna Nucleic Acids Research, Vol. 49, Issue 17 https://doi.org/10.1093/nar/gkab716	journal	August 2021
RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning Burley, Stephen K.; Bhikadiya, Charmi; Bi, Chunxiao Nucleic Acids Research, Vol. 51, Issue D1 https://doi.org/10.1093/nar/gkac1077	journal	November 2022
Structure-based investigations of the NAD+-II riboswitch Xu, Xiaochen; Egger, Michaela; Li, Chunyan Nucleic Acids Research, Vol. 51, Issue 1 https://doi.org/10.1093/nar/gkac1227	journal	January 2023
RNAspider: a webserver to analyze entanglements in RNA 3D structures Luwanski, Kamil; Hlushchenko, Vladyslav; Popenda, Mariusz Nucleic Acids Research, Vol. 50, Issue W1 https://doi.org/10.1093/nar/gkac218	journal	March 2022
AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences Varadi, Mihaly; Bertoni, Damian; Magana, Paulyna Nucleic Acids Research, Vol. 52, Issue D1 https://doi.org/10.1093/nar/gkad1011	journal	November 2023
Crystal structures of the NAD+-II riboswitch reveal two distinct ligand-binding pockets Peng, Xuemei; Liao, Wenjian; Lin, Xiaowei Nucleic Acids Research, Vol. 51, Issue 6 https://doi.org/10.1093/nar/gkad102	journal	February 2023
RNAJP: enhanced RNA 3D structure predictions with non-canonical interactions and global topology sampling Li, Jun; Chen, Shi-Jie Nucleic Acids Research, Vol. 51, Issue 7 https://doi.org/10.1093/nar/gkad122	journal	March 2023
Catalytic mechanism and pH dependence of a methyltransferase ribozyme (MTR1) from computational enzymology McCarthy, Erika; Ekesan, Şölen; Giese, Timothy J. Nucleic Acids Research, Vol. 51, Issue 9 https://doi.org/10.1093/nar/gkad260	journal	April 2023
WebTetrado: a webserver to explore quadruplexes in nucleic acid 3D structures Adamczyk, Bartosz; Zurkowski, Michal; Szachniuk, Marta Nucleic Acids Research, Vol. 51, Issue W1 https://doi.org/10.1093/nar/gkad346	journal	May 2023
Rfam: an RNA family database Griffiths-Jones, S. Nucleic Acids Research, Vol. 31, Issue 1 https://doi.org/10.1093/nar/gkg006	journal	January 2003
Tools for the automatic identification and classification of RNA base pairs Yang, H. Nucleic Acids Research, Vol. 31, Issue 13 https://doi.org/10.1093/nar/gkg529	journal	July 2003
Mfold web server for nucleic acid folding and hybridization prediction Zuker, M. Nucleic Acids Research, Vol. 31, Issue 13 https://doi.org/10.1093/nar/gkg595	journal	July 2003
Predicting RNA pseudoknot folding thermodynamics Cao, S.; Chen, S. -J. Nucleic Acids Research, Vol. 34, Issue 9 https://doi.org/10.1093/nar/gkl346	journal	May 2006
The Vienna RNA Websuite Gruber, A. R.; Lorenz, R.; Bernhart, S. H. Nucleic Acids Research, Vol. 36, Issue Web Server https://doi.org/10.1093/nar/gkn188	journal	May 2008
CENTROIDFOLD: a web server for RNA secondary structure prediction Sato, K.; Hamada, M.; Asai, K. Nucleic Acids Research, Vol. 37, Issue Web Server https://doi.org/10.1093/nar/gkp367	journal	May 2009
Automated 3D structure composition for large RNAs Popenda, Mariusz; Szachniuk, Marta; Antczak, Maciej Nucleic Acids Research, Vol. 40, Issue 14 https://doi.org/10.1093/nar/gks339	journal	April 2012
RNA Bricks—a database of RNA 3D motifs and their interactions Chojnowski, Grzegorz; Waleń, Tomasz; Bujnicki, Janusz M. Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1084	journal	November 2013
RNAlyzer—novel approach for quality analysis of RNA structural models Lukasiak, Piotr; Antczak, Maciej; Ratajczak, Tomasz Nucleic Acids Research, Vol. 41, Issue 12 https://doi.org/10.1093/nar/gkt318	journal	April 2013
3dRNAscore: a distance and torsion angle dependent evaluation function of 3D RNA structures Wang, Jian; Zhao, Yunjie; Zhu, Chunyan Nucleic Acids Research, Vol. 43, Issue 10 https://doi.org/10.1093/nar/gkv141	journal	February 2015
SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction Boniecki, Michal J.; Lach, Grzegorz; Dawson, Wayne K. Nucleic Acids Research, Vol. 44, Issue 7 https://doi.org/10.1093/nar/gkv1479	journal	December 2015
NPDock: a web server for protein–nucleic acid docking Tuszynska, Irina; Magnus, Marcin; Jonak, Katarzyna Nucleic Acids Research, Vol. 43, Issue W1 https://doi.org/10.1093/nar/gkv493	journal	May 2015
Identifying novel sequence variants of RNA 3D motifs Zirbel, Craig L.; Roll, James; Sweeney, Blake A. Nucleic Acids Research, Vol. 43, Issue 15 https://doi.org/10.1093/nar/gkv651	journal	June 2015
SimRNAweb: a web server for RNA 3D structure modeling with optional restraints Magnus, Marcin; Boniecki, Michał J.; Dawson, Wayne Nucleic Acids Research, Vol. 44, Issue W1 https://doi.org/10.1093/nar/gkw279	journal	April 2016
A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs Poblete, Simón; Bottaro, Sandro; Bussi, Giovanni Nucleic Acids Research, Vol. 46, Issue 4 https://doi.org/10.1093/nar/gkx1269	journal	December 2017
Optimization of RNA 3D structure prediction using evolutionary restraints of nucleotide–nucleotide interactions from direct coupling analysis Wang, Jian; Mao, Kangkun; Zhao, Yunjie Nucleic Acids Research, Vol. 45, Issue 11 https://doi.org/10.1093/nar/gkx386	journal	May 2017
RNAcentral: a hub of information for non-coding RNA sequences Sweeney, Blake A.; Petrov, Anton I.; Burkov, Boris Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky1034	journal	November 2018
RNAcentral: a hub of information for non-coding RNA sequences Sweeney, Blake A.; Petrov, Anton I.; Burkov, Boris Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky1206	journal	December 2018
Limits in accuracy and a strategy of RNA structure prediction using experimental information Wang, Jian; Williams, Benfeard; Chirasani, Venkata R. Nucleic Acids Research, Vol. 47, Issue 11 https://doi.org/10.1093/nar/gkz427	journal	May 2019
Structural basis for 2′-deoxyguanosine recognition by the 2′-dG-II class of riboswitches Matyjasik, Michal M.; Batey, Robert T. Nucleic Acids Research, Vol. 47, Issue 20 https://doi.org/10.1093/nar/gkz839	journal	October 2019
An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies Kelley, Lawrence A.; Gardner, Stephen P.; Sutcliffe, Michael J. "Protein Engineering, Design and Selection", Vol. 9, Issue 11 https://doi.org/10.1093/protein/9.11.1063	journal	January 1996
A solution for the best rotation to relate two sets of vectors Kabsch, W. Acta Crystallographica Section A, Vol. 32, Issue 5 https://doi.org/10.1107/S0567739476001873	journal	September 1976
The Protein Data Bank Berman, Helen M.; Battistuz, Tammy; Bhat, T. N. Acta Crystallographica Section D Biological Crystallography, Vol. 58, Issue 6 https://doi.org/10.1107/S0907444902003451	journal	May 2002
Blind protein structure prediction using accelerated free-energy simulations Perez, Alberto; Morrone, Joseph A.; Brini, Emiliano Science Advances, Vol. 2, Issue 11 https://doi.org/10.1126/sciadv.1601274	journal	November 2016
Blind prediction of noncanonical RNA structure at atomic accuracy Watkins, Andrew M.; Geniesse, Caleb; Kladwang, Wipapat Science Advances, Vol. 4, Issue 5 https://doi.org/10.1126/sciadv.aar5316	journal	May 2018
Zika virus produces noncoding RNAs using a multi-pseudoknot structure that confounds a cellular exonuclease Akiyama, B. M.; Laurence, H. M.; Massey, A. R. Science, Vol. 354, Issue 6316 https://doi.org/10.1126/science.aah3963	journal	November 2016
Geometric deep learning of RNA structure Townshend, Raphael J. L.; Eismann, Stephan; Watkins, Andrew M. Science, Vol. 373, Issue 6558 https://doi.org/10.1126/science.abe5650	journal	August 2021
Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome Bhatt, Pramod R.; Scaiola, Alain; Loughran, Gary Science, Vol. 372, Issue 6548 https://doi.org/10.1126/science.abf3546	journal	June 2021
RNAstructure: software for RNA secondary structure prediction and analysis Reuter, Jessica S.; Mathews, David H. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-129	journal	March 2010
ViennaRNA Package 2.0 Lorenz, Ronny; Bernhart, Stephan H.; Höner zu Siederdissen, Christian Algorithms for Molecular Biology, Vol. 6, Issue 1 https://doi.org/10.1186/1748-7188-6-26	journal	November 2011
QRNAS: software tool for refinement of nucleic acid structures Stasiewicz, Juliusz; Mukherjee, Sunandan; Nithin, Chandran BMC Structural Biology, Vol. 19, Issue 1 https://doi.org/10.1186/s12900-019-0103-1	journal	March 2019
RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction Cruz, J. A.; Blanchet, M. -F.; Boniecki, M. RNA, Vol. 18, Issue 4 https://doi.org/10.1261/rna.031054.111	journal	February 2012
Predicting structure and stability for RNA complexes with intermolecular loop–loop base-pairing Cao, Song; Xu, Xiaojun; Chen, Shi-Jie RNA, Vol. 20, Issue 6 https://doi.org/10.1261/rna.043976.113	journal	April 2014
RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures Miao, Zhichao; Adamiak, Ryszard W.; Blanchet, Marc-Frédérick RNA, Vol. 21, Issue 6 https://doi.org/10.1261/rna.049502.114	journal	April 2015
Solution structure of the 5′-terminal hairpin of the 7SK small nuclear RNA Bourbigot, Sarah; Dock-Bregeon, Anne-Catherine; Eberling, Pascal RNA, Vol. 22, Issue 12 https://doi.org/10.1261/rna.056523.116	journal	October 2016
RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme Miao, Zhichao; Adamiak, Ryszard W.; Antczak, Maciej RNA, Vol. 23, Issue 5 https://doi.org/10.1261/rna.060368.116	journal	January 2017
Structure and ligand binding of the ADP-binding domain of the NAD⁺ riboswitch Huang, Lin; Wang, Jia; Lilley, David M. J. RNA, Vol. 26, Issue 7 https://doi.org/10.1261/rna.074898.120	journal	April 2020
RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers Miao, Zhichao; Adamiak, Ryszard W.; Antczak, Maciej RNA, Vol. 26, Issue 8 https://doi.org/10.1261/rna.075341.120	journal	May 2020
Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions Carrascoza, Francisco; Antczak, Maciej; Miao, Zhichao RNA, Vol. 28, Issue 2 https://doi.org/10.1261/rna.078685.121	journal	November 2021
Crystal structure of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) frameshifting pseudoknot Jones, Christopher P.; Ferré-D'Amaré, Adrian R. RNA, Vol. 28, Issue 2 https://doi.org/10.1261/rna.078825.121	journal	November 2021
VfoldMCPX: predicting multistrand RNA complexes Zhang, Sicheng; Cheng, Yi; Guo, Peixuan RNA, Vol. 28, Issue 4 https://doi.org/10.1261/rna.079020.121	journal	January 2022
Predicting structures and stabilities for H-type pseudoknots with interhelix loops Cao, Song; Chen, Shi-Jie RNA, Vol. 15, Issue 4 https://doi.org/10.1261/rna.1429009	journal	February 2009
New metrics for comparing and assessing discrepancies between RNA 3D structures and models Parisien, M.; Cruz, J. A.; Westhof, E. RNA, Vol. 15, Issue 10 https://doi.org/10.1261/rna.1700409	journal	August 2009
ProbKnot: Fast prediction of RNA secondary structure including pseudoknots Bellaousov, S.; Mathews, D. H. RNA, Vol. 16, Issue 10 https://doi.org/10.1261/rna.2125310	journal	August 2010
Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms Ding, F.; Sharma, S.; Chalasani, P. RNA, Vol. 14, Issue 6 https://doi.org/10.1261/rna.894608	journal	April 2008
rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids Ruiz-Carmona, Sergio; Alvarez-Garcia, Daniel; Foloppe, Nicolas PLoS Computational Biology, Vol. 10, Issue 4 https://doi.org/10.1371/journal.pcbi.1003571	journal	April 2014
Vfold: A Web Server for RNA Structure and Folding Thermodynamics Prediction Xu, Xiaojun; Zhao, Peinan; Chen, Shi-Jie PLoS ONE, Vol. 9, Issue 9 https://doi.org/10.1371/journal.pone.0107504	journal	September 2014
Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers Pérez, Alberto; Marchán, Iván; Svozil, Daniel Biophysical Journal, Vol. 92, Issue 11 https://doi.org/10.1529/biophysj.106.097782	journal	June 2007
RNApolis: Computational Platform for RNA Structure Analysis Szachniuk, Marta Foundations of Computing and Decision Sciences, Vol. 44, Issue 2 https://doi.org/10.2478/fcds-2019-0012	journal	June 2019
RNA 3D Structure Prediction Using Coarse-Grained Models Li, Jun; Chen, Shi-Jie Frontiers in Molecular Biosciences, Vol. 8 https://doi.org/10.3389/fmolb.2021.720937	journal	July 2021
Length-Dependent Deep Learning Model for RNA Secondary Structure Prediction Mao, Kangkun; Wang, Jun; Xiao, Yi Molecules, Vol. 27, Issue 3 https://doi.org/10.3390/molecules27031030	journal	February 2022
Structures and Functions of Viral 5′ Non-Coding Genomic RNA Domain-I in Group-B Enterovirus Infections Glenet, Marie; Heng, Laetitia; Callon, Domitille Viruses, Vol. 12, Issue 9 https://doi.org/10.3390/v12090919	journal	August 2020

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