{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T14:52:57Z","timestamp":1791298377204,"version":"4.1.0"},"reference-count":0,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T00:00:00Z","timestamp":1791244800000},"content-version":"am","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>We present RAFA, a C\u2009++ command-line tool for RNA all-atom structure reconstruction from sparse or partial coordinates. RAFA targets settings in which coarse-grained modelling, low-resolution fitting, or partial experimental interpretation provides RNA anchor atoms but not a complete atomic model. The method retrieves experimentally observed 3\u20135\u2009nt all-atom RNA fragments, fits them to local anchors, combines overlapping fragment-derived coordinate estimates by weighted consensus, and routes sparse and rich inputs through distinct reconstruction paths. In an independent RNA3DB train\/test evaluation, no library\u2013test pair exceeded 80% global sequence identity. RAFA achieved lower all-atom root-mean-square deviation (RMSD) values than Arena in 73.3% of target\u2013mode comparisons, with the largest gains in input modes with the fewest structural constraints.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>RAFA is available at https:\/\/github.com\/wangleiofficial\/RAFA and archived at https:\/\/doi.org\/10.5281\/zenodo.20951205.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag746","type":"journal-article","created":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T11:32:01Z","timestamp":1791286321000},"source":"Crossref","is-referenced-by-count":0,"title":["RAFA: RNA all-atom structure reconstruction from sparse anchor coordinates"],"prefix":"10.1093","author":[{"given":"Lei","family":"Wang","sequence":"first","affiliation":[{"name":"Central China Normal University State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, , Wuhan 430079,","place":["China"]},{"name":"Huazhong University of Science and Technology School of Software Engineering, , Luoyu Road 1037, Wuhan 430074,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zilu","family":"Zeng","sequence":"additional","affiliation":[{"name":"Wuhan Children\u2019s Hospital, Tongji Medical College, Huazhong University of Science and Technology , Hongkong Road, 430070, Wuhan,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,10,6]]},"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btag746\/71627602\/btag746.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btag746\/71627602\/btag746.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T14:30:59Z","timestamp":1791297059000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article\/doi\/10.1093\/bioinformatics\/btag746\/8869022"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10,6]]},"references-count":0,"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btag746","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,6]]},"article-number":"btag746"}}