{"doi":"10.1038/s41592-024-02487-0","title":"Accurate RNA 3D structure prediction using a language model-based deep learning approach","abstract":"Accurate prediction of RNA three-dimensional (3D) structures remains an unsolved challenge. Determining RNA 3D structures is crucial for understanding their functions and informing RNA-targeting drug development and synthetic biology design. The structural flexibility of RNA, which leads to the scarcity of experimentally determined data, complicates computational prediction efforts. Here we present RhoFold+, an RNA language model-based deep learning method that accurately predicts 3D structures of single-chain RNAs from sequences. By integrating an RNA language model pretrained on ~23.7 million RNA sequences and leveraging techniques to address data scarcity, RhoFold+ offers a fully automated end-to-end pipeline for RNA 3D structure prediction. Retrospective evaluations on RNA-Puzzles and CASP15 natural RNA targets demonstrate the superiority of RhoFold+ over existing methods, including human expert groups. Its efficacy and generalizability are further validated through cross-family and cross-type assessments, as well as time-censored benchmarks. Additionally, RhoFold+ predicts RNA secondary structures and interhelical angles, providing empirically verifiable features that broaden its applicability to RNA structure and function studies.","journal":"Nature Methods","year":2024,"id":416243,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":198,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9349,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1199337,"name":"Zhihang Hu","orcid":"0000-0003-4947-2140","position":1,"is_corresponding":false},{"id":1199338,"name":"Siqi Sun","orcid":"0000-0001-7240-8724","position":2,"is_corresponding":false},{"id":588230,"name":"Di Liu","orcid":"0000-0002-0708-7466","position":3,"is_corresponding":false},{"id":562039,"name":"Felix Wong","orcid":"0000-0002-2309-8835","position":4,"is_corresponding":false},{"id":1199339,"name":"Jiuming Wang","orcid":"0009-0003-9591-156X","position":5,"is_corresponding":false},{"id":1199340,"name":"Jiayang Chen","orcid":"0000-0002-0056-088X","position":6,"is_corresponding":false},{"id":1199341,"name":"Yixuan Wang","orcid":"0000-0002-0606-8263","position":7,"is_corresponding":false},{"id":1199342,"name":"Liang Hong","orcid":"0000-0003-0107-336X","position":8,"is_corresponding":false},{"id":1199343,"name":"Jin Xiao","orcid":"0000-0001-5059-1492","position":9,"is_corresponding":false},{"id":1199344,"name":"Liangzhen Zheng","orcid":"0000-0003-1179-2106","position":10,"is_corresponding":false},{"id":1200454,"name":"Tejas Krishnamoorthi","orcid":null,"position":11,"is_corresponding":false},{"id":1199345,"name":"Irwin King","orcid":"0000-0001-8106-6447","position":12,"is_corresponding":false},{"id":1199346,"name":"Sheng Wang","orcid":"0000-0003-4210-1670","position":13,"is_corresponding":false},{"id":44857,"name":"Peng Yin","orcid":"0000-0002-2769-6357","position":14,"is_corresponding":false},{"id":31916,"name":"James J. Collins","orcid":"0000-0002-5560-8246","position":15,"is_corresponding":false},{"id":571662,"name":"Yu Li","orcid":"0000-0002-3664-6722","position":16,"is_corresponding":false},{"id":259334,"name":"Tao Shen","orcid":"0000-0002-6129-3092","position":0,"is_corresponding":true}],"reference_count":60,"raw_metadata":null,"created_at":"2026-07-19T01:56:20.964471Z","pmid":"39572716","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}