{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T04:10:38Z","timestamp":1779336638964,"version":"3.51.4"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2026,4,28]],"date-time":"2026-04-28T00:00:00Z","timestamp":1777334400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["1R35GM137974"],"award-info":[{"award-number":["1R35GM137974"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,5,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Breakthrough advancements in protein tertiary and quaternary structure prediction have accelerated structural bioinformatics research activity and drug development processes. However, many biological mechanisms involve more complicated interactions, such as those between amino and nucleic acids. Predicting the structure of protein\u2013RNA complexes is highly relevant and challenging due to data scarcity and experimental difficulties. Understanding and interpreting these interactions can yield crucial insights into various human diseases and biological phenomena. Thus, quality assessment methods that specifically evaluate protein\u2013RNA complex models can provide significant utility in this emerging area of protein\u2013RNA structural bioinformatics research.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We propose a novel graph transformer-based approach named complex quality assessment of RNA and protein (CARP) to infer multiple quality perspectives of protein\u2013RNA complex models. For a single protein\u2013RNA complex model, in one shot, CARP simultaneously predicts multiple overall fold, overall interface, and per-protein\u2013RNA interface quality estimates. When evaluated against a non-redundant protein\u2013RNA docking benchmark, our methods demonstrated obvious improved performance compared to almost all of the existing scoring tools, particularly when ordering and selecting the highest quality decoys. Furthermore, CARP consistently selected higher quality models relative to other predictors when tested on CASP16 targets. Specifically, CARP-predicted global interface and global protein\u2013RNA interface qualities were ranked first and second, respectively, based on the selected top-3 models over all ten CASP16 protein\u2013RNA complex targets. CARP also showed a strong ability, compared to both existing tools and AlphaFold3 self-estimates, in selecting high quality AlphaFold3 models.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>CARP is freely available at github.com\/zwang-bioinformatics\/CARP\/.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag202","type":"journal-article","created":{"date-parts":[[2026,4,22]],"date-time":"2026-04-22T11:50:32Z","timestamp":1776858632000},"source":"Crossref","is-referenced-by-count":0,"title":["Inferring the qualities of protein\u2013RNA models with graph transformers"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-1464-3583","authenticated-orcid":false,"given":"Andrew Jordan","family":"Siciliano","sequence":"first","affiliation":[{"name":"Department of Computer Science, University of Miami , Coral Gables, FL 33124,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-9157-3440","authenticated-orcid":false,"given":"Yifan","family":"Bao","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Miami , Coral Gables, FL 33124,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-8330-4348","authenticated-orcid":false,"given":"Bishal","family":"Shrestha","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Miami , Coral Gables, FL 33124,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3892-6151","authenticated-orcid":false,"given":"Zheng","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Miami , Coral Gables, FL 33124,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2026,4,28]]},"reference":[{"key":"2026052023583511600_btag202-B1","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1038\/s41586-024-07487-w","article-title":"Accurate structure prediction of biomolecular interactions with AlphaFold 3","volume":"630","author":"Abramson","year":"2024","journal-title":"Nature"},{"key":"2026052023583511600_btag202-B2","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1107\/S0907444913007051","article-title":"Openstructure: an integrated software framework for computational structural biology","volume":"69","author":"Biasini","year":"2013","journal-title":". 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