{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T10:12:31Z","timestamp":1788775951879,"version":"build-2803163510"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T00:00:00Z","timestamp":1788739200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62473257"],"award-info":[{"award-number":["62473257"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62573293"],"award-info":[{"award-number":["62573293"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003399","name":"Science and Technology Commission of Shanghai Municipality","doi-asserted-by":"publisher","award":["24ZR1435300"],"award-info":[{"award-number":["24ZR1435300"]}],"id":[{"id":"10.13039\/501100003399","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003399","name":"Science and Technology Commission of Shanghai Municipality","doi-asserted-by":"publisher","award":["22511104100"],"award-info":[{"award-number":["22511104100"]}],"id":[{"id":"10.13039\/501100003399","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>While protein\u2013RNA interactions are fundamental to post-transcriptional processes, achieving a holistic understanding of their regulatory logic remains challenging. Current computational models often treat binding affinity, interface mapping, and RNA design as isolated tasks, thereby failing to provide a unified perspective of the protein\u2013RNA interactome. Here, we introduce ProRB, a unified sequence-based framework that jointly estimates protein\u2013RNA binding affinity, predicts binding interfaces in proteins and RNAs, and generates protein-binding RNA sequences from protein sequences. By fusing protein and RNA embeddings from language models via adaptive cross-modal attention, ProRB learns contextual and relational features for predicting protein\u2013RNA binding affinity and interface contacts, outperforming or achieving competitive performance compared to structure-based methods. Notably, its cross-attention maps reveal interpretable, motif-centric binding logic hidden in protein\u2013RNA interactions. Building on this interpretability, ProRB enables computationally prioritized design of protein-binding RNA sequences with enhanced biophysical properties and functional motifs. By unifying the prediction, interpretation, and generation tasks, ProRB provides a scalable unified model for decoding the protein\u2013RNA interaction and engineering motif-guided RNA therapeutics.<\/jats:p>","DOI":"10.1093\/nar\/gkag870","type":"journal-article","created":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T11:34:08Z","timestamp":1788521648000},"source":"Crossref","is-referenced-by-count":0,"title":["ProRB: a structure-free unified framework for joint prediction and design of protein\u2013RNA interactions"],"prefix":"10.1093","volume":"54","author":[{"given":"Yiming","family":"Xue","sequence":"first","affiliation":[{"name":"Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China , Shanghai 200240 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaojian","family":"Liu","sequence":"additional","affiliation":[{"name":"Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China , Shanghai 200240 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weimin","family":"Zhu","sequence":"additional","affiliation":[{"name":"Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China , Shanghai 200240 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shengfan","family":"Wang","sequence":"additional","affiliation":[{"name":"Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China , Shanghai 200240 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4029-3325","authenticated-orcid":false,"given":"Hong-Bin","family":"Shen","sequence":"additional","affiliation":[{"name":"Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China , Shanghai 200240 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5010-464X","authenticated-orcid":false,"given":"Xiaoyong","family":"Pan","sequence":"additional","affiliation":[{"name":"Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China , Shanghai 200240 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