{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T23:20:29Z","timestamp":1775690429402,"version":"3.50.1"},"reference-count":64,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2022,6,25]],"date-time":"2022-06-25T00:00:00Z","timestamp":1656115200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"publisher","award":["DP210101875"],"award-info":[{"award-number":["DP210101875"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,8,10]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Recently, AlphaFold2 achieved high experimental accuracy for the majority of proteins in Critical Assessment of Structure Prediction (CASP 14). This raises the hope that one day, we may achieve the same feat for RNA structure prediction for those structured RNAs, which is as fundamentally and practically important similar to protein structure prediction. One major factor in the recent advancement of protein structure prediction is the highly accurate prediction of distance-based contact maps of proteins.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Here, we showed that by integrated deep learning with physics-inferred secondary structures, co-evolutionary information and multiple sequence-alignment sampling, we can achieve RNA contact-map prediction at a level of accuracy similar to that in protein contact-map prediction. More importantly, highly accurate prediction for top L long-range contacts can be assured for those RNAs with a high effective number of homologous sequences (Neff\u2009&amp;gt;\u200950). The initial use of the predicted contact map as distance-based restraints confirmed its usefulness in 3D structure prediction.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>SPOT-RNA-2D is available as a web server at https:\/\/sparks-lab.org\/server\/spot-rna-2d\/ and as a standalone program at https:\/\/github.com\/jaswindersingh2\/SPOT-RNA-2D.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac421","type":"journal-article","created":{"date-parts":[[2022,6,25]],"date-time":"2022-06-25T12:42:19Z","timestamp":1656160939000},"page":"3900-3910","source":"Crossref","is-referenced-by-count":24,"title":["Predicting RNA distance-based contact maps by integrated deep learning on physics-inferred secondary structure and evolutionary-derived mutational coupling"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0478-5533","authenticated-orcid":false,"given":"Jaswinder","family":"Singh","sequence":"first","affiliation":[{"name":"Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University , Brisbane, QLD 4111, Australia"}]},{"given":"Kuldip","family":"Paliwal","sequence":"additional","affiliation":[{"name":"Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University , Brisbane, QLD 4111, Australia"}]},{"given":"Thomas","family":"Litfin","sequence":"additional","affiliation":[{"name":"Institute for Glycomics, Griffith University , Parklands Dr. Southport, QLD 4222, Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4974-5188","authenticated-orcid":false,"given":"Jaspreet","family":"Singh","sequence":"additional","affiliation":[{"name":"Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University , Brisbane, QLD 4111, Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9958-5699","authenticated-orcid":false,"given":"Yaoqi","family":"Zhou","sequence":"additional","affiliation":[{"name":"Institute for Glycomics, Griffith University , Parklands Dr. Southport, QLD 4222, Australia"},{"name":"Institute for Systems and Physical Biology, Shenzhen Bay Laboratory , Shenzhen 518055, China"},{"name":"Peking University Shenzhen Graduate School, Peking University , Shenzhen 518055, China"}]}],"member":"286","published-online":{"date-parts":[[2022,6,25]]},"reference":[{"key":"2023041408492553400_","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"2023041408492553400_","author":"Ba","year":"2016"},{"key":"2023041408492553400_","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1126\/science.abj8754","article-title":"Accurate prediction of protein structures and interactions using a three-track neural network","volume":"373","author":"Baek","year":"2021","journal-title":"Science"},{"key":"2023041408492553400_","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1002\/prot.22934","article-title":"Learning generative models for protein fold families","volume":"79","author":"Balakrishnan","year":"2011","journal-title":"Proteins Struct. 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