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Accurate prediction of RNA three-dimensional (3D) structure remains an unsolved challenge.
Rfam: an rna family database
Sam Griffiths-Jones, Alex Bateman, Mhairi Marshall, Ajay Khanna, and Sean R Eddy · 2003
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Scoring function for automated assessment of protein structure template quality
Yang Zhang and Jeffrey Skolnick · 2004
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Tm-align: a protein structure alignment algorithm based on the tm-score
Yang Zhang and Jeffrey Skolnick · 2005
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Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
Weizhong Li and Adam Godzik · 2006
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Visualizing spatially correlated dynamics that directs rna conformational transitions
Qi Zhang, Andrew C Stelzer, Charles K Fisher, and Hashim M Al-Hashimi · 2007
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Predicting rna structure by multiple template homology modeling
Samuel C Flores, Yaqi Wan, Rick Russell, and Russ B Altman · 2010
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Moderna: a tool for comparative modeling of rna 3d structure
Magdalena Rother, Kristian Rother, Tomasz Puton, and Janusz M Bujnicki · 2011
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Rna-puzzles: a casp-like evaluation of rna three-dimensional structure prediction
José Almeida Cruz, Marc-Frédérick Blanchet, Michal Boniecki, Janusz M Bujnicki, Shi-Jie Chen, Song Cao, Rhiju Das, Feng Ding, Nikolay V Dokholyan, Samuel Coulbourn Flores, et al · 2012
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lddt: a local superposition-free score for comparing protein structures and models using distance difference tests
Valerio Mariani, Marco Biasini, Alessandro Barbato, and Torsten Schwede · 2013
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Infernal 1.1: 100-fold faster rna homology searches
Eric P Nawrocki and Sean R Eddy · 2013
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An overview of the amber biomolecular simulation package
Romelia Salomon-Ferrer, David A Case, and Ross C Walker · 2013
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Insights into rna structure and function from genome-wide studies
Stefanie A Mortimer, Mary Anne Kidwell, and Jennifer A Doudna · 2014
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Rna secondary structure modeling at consistent high accuracy using differential shape
Greggory M Rice, Christopher W Leonard, and Kevin M Weeks · 2014
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Rna-puzzles round ii: assessment of rna structure prediction programs applied to three large rna structures
Zhichao Miao, Ryszard W Adamiak, Marc-Frédérick Blanchet, Michal Boniecki, Janusz M Bujnicki, Shi-Jie Chen, Clarence Cheng, Grzegorz Chojnowski, Fang-Chieh Chou, Pablo Cordero, et al · 2015
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Metal ion-mediated nucleobase recognition by the ztp riboswitch
Jeremiah J Trausch, Joan G Marcano-Velázquez, Michal M Matyjasik, and Robert T Batey · 2015
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Simrna: a coarse-grained method for rna folding simulations and 3d structure prediction
Michal J Boniecki, Grzegorz Lach, Wayne K Dawson, Konrad Tomala, Pawel Lukasz, Tomasz Soltysinski, Kristian M Rother, and Janusz M Bujnicki · 2016
Earlier work this paper cites.
Automated rna 3d structure prediction with rnacomposer
Marcin Biesiada, Katarzyna J Purzycka, Marta Szachniuk, Jacek Blazewicz, and Ryszard W Adamiak · 2016
Earlier work this paper cites.
Rna-puzzles round iii: 3d rna structure prediction of five riboswitches and one ribozyme
Zhichao Miao, Ryszard W Adamiak, Maciej Antczak, Robert T Batey, Alexander J Becka, Marcin Biesiada, Michał J Boniecki, Janusz M Bujnicki, Shi-Jie Chen, Clarence Yu Cheng, et al · 2017
Cited alongside, same era.
Attention is all you need
Ashish Vaswani, Noam Shazeer, Niki Parmar, Jakob Uszkoreit, Llion Jones, Aidan N Gomez, Łukasz Kaiser, and Illia Polosukhin · 2017
Cited alongside, same era.
Principles for targeting rna with drug-like small molecules
Katherine Deigan Warner, Christine E Hajdin, and Kevin M Weeks · 2018
Cited alongside, same era.
Pervasive tertiary structure in the dengue virus rna genome
Elizabeth A Dethoff, Mark A Boerneke, Nandan S Gokhale, Brejnev M Muhire, Darren P Martin, Matthew T Sacco, Michael J McFadden, Jules B Weinstein, William B Messer, Stacy M Horner, et al · 2018
Cited alongside, same era.
3drna v2.0: An updated web server for rna 3d structure prediction
Jun Wang, Jian Wang, Yanzhao Huang, and Yi Xiao · 2019
Cited alongside, same era.
Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences
Alexander Rives, Joshua Meier, Tom Sercu, Siddharth Goyal, Zeming Lin, Jason Liu, Demi Guo, Myle Ott, C Lawrence Zitnick, Jerry Ma, et al · 2021
Later among the works it cites.
Pairing a high-resolution statistical potential with a nucleobase-centric sampling algorithm for improving rna model refinement
Peng Xiong, Ruibo Wu, Jian Zhan, and Yaoqi Zhou · 2021
Later among the works it cites.
Rna-responsive elements for eukaryotic translational control
Evan M Zhao, Angelo S Mao, Helena de Puig, Kehan Zhang, Nathaniel D Tippens, Xiao Tan, F Ran, Isaac Han, Peter Q Nguyen, Emma J Chory, et al · 2022
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Sub-3-å cryo-em structure of rna enabled by engineered homomeric self-assembly
Di Liu, François A Thélot, Joseph A Piccirilli, Maofu Liao, and Peng Yin · 2022
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Recent advances in RNA structurome
Bingbing Xu, Yanda Zhu, Changchang Cao, Hao Chen, Qiongli Jin, Guangnan Li, Junfeng Ma, Siwy Ling Yang, Jieyu Zhao, Jianghui Zhu, Yiliang Ding, Xianyang Fang, Yongfeng Jin, Chun Kit Kwok, Aiming Ren, Yue Wan, Zhiye Wang, Yuanchao Xue, Huakun Zhang, Qiangfeng Cliff Zhang, and Yu Zhou · 2022
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Rna secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning
Jaswinder Singh, Jack Hanson, Kuldip Paliwal, and Yaoqi Zhou · 2019
Cited alongside, same era.
Bert: Pre-training of deep bidirectional transformers for language understanding
Jacob Devlin Ming-Wei Chang Kenton and Lee Kristina Toutanova · 2019
Cited alongside, same era.
Farfar2: improved de novo rosetta prediction of complex global rna folds
Andrew Martin Watkins, Ramya Rangan, and Rhiju Das · 2020
Cited alongside, same era.
Rna secondary structure prediction by learning unrolled algorithms
Xinshi Chen, Yu Li, Ramzan Umarov, Xin Gao, and Le Song · 2020
Cited alongside, same era.
Rna-puzzles round iv: 3d structure predictions of four ribozymes and two aptamers
Zhichao Miao, Ryszard W Adamiak, Maciej Antczak, Michał J Boniecki, Janusz Bujnicki, Shi-Jie Chen, Clarence Yu Cheng, Yi Cheng, Fang-Chieh Chou, Rhiju Das, et al · 2020
Cited alongside, same era.
Rna-puzzles toolkit: a computational resource of rna 3d structure benchmark datasets, structure manipulation, and evaluation tools
Marcin Magnus, Maciej Antczak, Tomasz Zok, Jakub Wiedemann, Piotr Lukasiak, Yang Cao, Janusz M Bujnicki, Eric Westhof, Marta Szachniuk, and Zhichao Miao · 2020
Cited alongside, same era.
Structural insights into rna dimerization: motifs, interfaces and functions
Charles Bou-Nader and Jinwei Zhang · 2020
Cited alongside, same era.
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Jiayang Chen, Zhihang Hu, Siqi Sun, Qingxiong Tan, Yixuan Wang, Qinze Yu, Licheng Zong, Liang Hong, Jin Xiao, Irwin King, et al · 2022
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De novo rna tertiary structure prediction at atomic resolution using geometric potentials from deep learning
Robin Pearce, Gilbert S Omenn, and Yang Zhang · 2022
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E2efold-3d: end-to-end deep learning method for accurate de novo rna 3d structure prediction
Tao Shen, Zhihang Hu, Zhangzhi Peng, Jiayang Chen, Peng Xiong, Liang Hong, Liangzhen Zheng, Yixuan Wang, Irwin King, Sheng Wang, et al · 2022
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Alternative rna conformations: Companion or combatant
Payal Gupta, Rushikesh M Khadake, Shounok Panja, Krushna Shinde, and Ambadas B Rode · 2022
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Ufold: fast and accurate rna secondary structure prediction with deep learning
Laiyi Fu, Yingxin Cao, Jie Wu, Qinke Peng, Qing Nie, and Xiaohui Xie · 2022
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trrosettarna: automated prediction of rna 3d structure with transformer network
Wenkai Wang, Chenjie Feng, Renmin Han, Ziyi Wang, Lisha Ye, Zongyang Du, Hong Wei, Fa Zhang, Zhenling Peng, and Jianyi Yang · 2023
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Accurate prediction of protein–nucleic acid complexes using rosettafoldna
Minkyung Baek, Ryan McHugh, Ivan Anishchenko, Hanlun Jiang, David Baker, and Frank DiMaio · 2023
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Integrating end-to-end learning with deep geometrical potentials for ab initio rna structure prediction
Yang Li, Chengxin Zhang, Chenjie Feng, Robin Pearce, P Lydia Freddolino, and Yang Zhang · 2023
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Assessment of three-dimensional rna structure prediction in casp15
Rhiju Das, Rachael C Kretsch, Adam J Simpkin, Thomas Mulvaney, Phillip Pham, Ramya Rangan, Fan Bu, Ronan Keegan, Maya Topf, Daniel Rigden, et al · 2023
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Visualizing rna conformational and architectural heterogeneity in solution
Jienyu Ding, Yun-Tzai Lee, Yuba Bhandari, Charles D Schwieters, Lixin Fan, Ping Yu, Sergey G Tarosov, Jason R Stagno, Buyong Ma, Ruth Nussinov, et al · 2023
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Accurate structure prediction of biomolecular interactions with alphafold 3
Josh Abramson, Jonas Adler, Jack Dunger, Richard Evans, Tim Green, Alexander Pritzel, Olaf Ronneberger, Lindsay Willmore, Andrew J Ballard, Joshua Bambrick, et al · 2024
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