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We introduce RNA-FrameFlow, the first generative model for 3D RNA backbone design.
Ribose puckering: structure, dynamics, energetics, and the pseudorotation cycle
Stephen C Harvey and M Prabhakaran · 1986
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Geometric parameters in nucleic acids: sugar and phosphate constituents
Anke Gelbin, Bohdan Schneider, Lester Clowney, Shu-Hsin Hsieh, Wilma K Olson, and Helen M Berman · 1996
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Therapeutic applications of ribozymes and riboswitches
Jerome Mulhbacher, Patrick St-Pierre, and Daniel A Lafontaine · 2010
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A new way to see rna
Kevin S Keating, Elisabeth L Humphris, and Anna Marie Pyle · 2011
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The new frontier of genome engineering with crispr-cas9
Jennifer A Doudna and Emmanuelle Charpentier · 2014
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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
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Resolving sugar puckers in rna excited states exposes slow modes of repuckering dynamics
Mary C Clay, Laura R Ganser, Dawn K Merriman, and Hashim M Al-Hashimi · 2017
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Single-stranded dna and rna origami
Dongran Han, Xiaodong Qi, Cameron Myhrvold, Bei Wang, Mingjie Dai, Shuoxing Jiang, Maxwell Bates, Yan Liu, Byoungkwon An, Fei Zhang, et al · 2017
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The roles of structural dynamics in the cellular functions of rnas
Laura R Ganser, Megan L Kelly, Daniel Herschlag, and Hashim M Al-Hashimi · 2019
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Computational design of three-dimensional rna structure and function
Joseph D Yesselman, Daniel Eiler, Erik D Carlson, Michael R Gotrik, Anne E d’Aquino, Alexandra N Ooms, Wipapat Kladwang, Paul D Carlson, Xuesong Shi, David A Costantino, et al · 2019
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Farfar2: improved de novo rosetta prediction of complex global rna folds
Andrew Martin Watkins, Ramya Rangan, and Rhiju Das · 2020
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The limitless future of rna therapeutics
Tulsi Ram Damase, Roman Sukhovershin, Christian Boada, Francesca Taraballi, Roderic I Pettigrew, and John P Cooke · 2021
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Highly accurate protein structure prediction with AlphaFold
John Jumper, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger, Kathryn Tunyasuvunakool, Russ Bates, Augustin Zidek, Anna Potapenko, et al · 2021
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Geometric deep learning of rna structure
Raphael JL Townshend, Stephan Eismann, Andrew M Watkins, Ramya Rangan, Maria Karelina, Rhiju Das, and Ron O Dror · 2021
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RNAsolo: a repository of cleaned PDB-derived RNA 3D structures
Bartosz Adamczyk, Maciej Antczak, and Marta Szachniuk · 2022
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Robust deep learning–based protein sequence design using proteinmpnn
Justas Dauparas, Ivan Anishchenko, Nathaniel Bennett, Hua Bai, Robert J Ragotte, Lukas F Milles, Basile IM Wicky, Alexis Courbet, Rob J de Haas, Neville Bethel, et al · 2022
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Illuminating protein space with a programmable generative model
John Ingraham, Max Baranov, Zak Costello, Vincent Frappier, Ahmed Ismail, Shan Tie, Wujie Wang, Vincent Xue, Fritz Obermeyer, Andrew Beam, et al · 2022
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Code of opencomplex
Yu Jingcheng, Chen Zhaoming, Li Zhaoqun, Zeng Mingliang, Lin Wenjun, Huang He, and Ye Qiwei · 2022
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E2efold-3d: End-to-end deep learning method for accurate de novo rna 3d structure prediction, 2022
Tao Shen, Zhihang Hu, Zhangzhi Peng, Jiayang Chen, Peng Xiong, Liang Hong, Liangzhen Zheng, Yixuan Wang, Irwin King, Sheng Wang, Siqi Sun, and Yu Li · 2022
Cited alongside, same era.
De novo design of protein structure and function with rfdiffusion
Joseph L Watson, David Juergens, Nathaniel R Bennett, Brian L Trippe, Jason Yim, Helen E Eisenach, Woody Ahern, Andrew J Borst, Robert J Ragotte, Lukas F Milles, 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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Chai-1: Decoding the molecular interactions of life
Jacques Boitreaud, Jack Dent, Matthew McPartlon, Joshua Meier, Vinicius Reis, Alex Rogozhnikov, and Kevin Wu · 2024
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Flow matching on general geometries, 2024
Ricky T. Q. Chen and Yaron Lipman · 2024
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Alexander Denker, Francisco Vargas, Shreyas Padhy, Kieran Didi, Simon Mathis, Vincent Dutordoir, Riccardo Barbano, Emile Mathieu, Urszula Julia Komorowska, and Pietro Lio · 2024
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Thoughts on how to think (and talk) about rna structure
Quentin Vicens and Jeffrey S Kieft · 2022
Cited alongside, same era.
Us-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes
Chengxin Zhang, Morgan Shine, Anna Marie Pyle, and Yang Zhang · 2022
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Se(3)-stochastic flow matching for protein backbone generation, 2023
Avishek Joey Bose, Tara Akhound-Sadegh, Kilian Fatras, Guillaume Huguet, Jarrid Rector-Brooks, Cheng-Hao Liu, Andrei Cristian Nica, Maksym Korablyov, Michael Bronstein, and Alexander Tong · 2023
Cited alongside, same era.
A framework for conditional diffusion modelling with applications in motif scaffolding for protein design
Kieran Didi, Francisco Vargas, Simon Mathis, Vincent Dutordoir, Emile Mathieu, Urszula Julia Komorowska, and Pietro Lio · 2023
Cited alongside, same era.
Rna target highlights in casp15: Evaluation of predicted models by structure providers
Rachael C Kretsch, Ebbe S Andersen, Janusz M Bujnicki, Wah Chiu, Rhiju Das, Bingnan Luo, Benoît Masquida, Ewan KS McRae, Griffin M Schroeder, Zhaoming Su, et al · 2023
Cited alongside, same era.
Generating novel, designable, and diverse protein structures by equivariantly diffusing oriented residue clouds, 2023
Yeqing Lin and Mohammed AlQuraishi · 2023
Cited alongside, same era.
Towards joint sequence-structure generation of nucleic acid and protein complexes with se(3)-discrete diffusion, 2023
Alex Morehead, Jeffrey Ruffolo, Aadyot Bhatnagar, and Ali Madani · 2023
Cited alongside, same era.
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Ribonanza: deep learning of rna structure through dual crowdsourcing
Shujun He, Rui Huang, Jill Townley, Rachael C Kretsch, Thomas G Karagianes, David BT Cox, Hamish Blair, Dmitry Penzar, Valeriy Vyaltsev, Elizaveta Aristova, et al · 2024
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Tailor made: the art of therapeutic mrna design
Mihir Metkar, Christopher S Pepin, and Melissa J Moore · 2024
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Rnaflow: Rna structure & sequence co-design via inverse folding-based flow matching
Divya Nori and Wengong Jin · 2024
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Rinalmo: General-purpose rna language models can generalize well on structure prediction tasks
Rafael Josip Penic, Tin Vlasic, Roland G Huber, Yue Wan, and Mile Sikic · 2024
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Rna language models predict mutations that improve rna function
Yekaterina Shulgina, Marena I Trinidad, Conner J Langeberg, Hunter Nisonoff, Seyone Chithrananda, Petr Skopintsev, Amos J Nissley, Jaymin Patel, Ron S Boger, Honglue Shi, et al · 2024
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The landscape of rna 3d structure modeling with transformer networks
Sumit Tarafder, Rahmatullah Roche, and Debswapna Bhattacharya · 2024
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Practical and asymptotically exact conditional sampling in diffusion models
Luhuan Wu, Brian Trippe, Christian Naesseth, David Blei, and John P Cunningham · 2024
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gRNAde: Geometric deep learning for 3d rna inverse design
Chaitanya K. Joshi, Arian R. Jamasb, Ramon Viñas, Charles Harris, Simon Mathis, Alex Morehead, Rishabh Anand, and Pietro Liò · 2025
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