{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,5]],"date-time":"2026-04-05T08:57:02Z","timestamp":1775379422474,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2022,6,8]],"date-time":"2022-06-08T00:00:00Z","timestamp":1654646400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004239","name":"Poznan University of Technology","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004239","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100020811","name":"Institute of Bioorganic Chemistry PAS","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100020811","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004281","name":"National Science Centre","doi-asserted-by":"publisher","award":["2019\/35\/B\/ST6\/03074"],"award-info":[{"award-number":["2019\/35\/B\/ST6\/03074"]}],"id":[{"id":"10.13039\/501100004281","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,7,11]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>The development of algorithms dedicated to RNA three-dimensional (3D) structures contributes to the demand for training, testing and benchmarking data. A reliable source of such data derived from computational prediction is the RNA-Puzzles repository. In contrast, the largest resource with experimentally determined structures is the Protein Data Bank. However, files in this archive often contain other molecular data in addition to the RNA structure itself, which\u2014to be used by RNA processing algorithms\u2014should be removed.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>RNAsolo is a self-updating database dedicated to RNA bioinformatics. It systematically collects experimentally determined RNA 3D structures stored in the PDB, cleans them from non-RNA chains, and groups them into equivalence classes. It allows users to download various subsets of data\u2014clustered by resolution, source, data format, etc.\u2014for further processing and analysis with a single click.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>The repository is publicly available at https:\/\/rnasolo.cs.put.poznan.pl.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac386","type":"journal-article","created":{"date-parts":[[2022,6,8]],"date-time":"2022-06-08T12:09:55Z","timestamp":1654690195000},"page":"3668-3670","source":"Crossref","is-referenced-by-count":54,"title":["RNAsolo: a repository of cleaned PDB-derived RNA 3D structures"],"prefix":"10.1093","volume":"38","author":[{"given":"Bartosz","family":"Adamczyk","sequence":"first","affiliation":[{"name":"Institute of Computing Science, Poznan University of Technology , 60-965 Poznan, Poland"}]},{"given":"Maciej","family":"Antczak","sequence":"additional","affiliation":[{"name":"Institute of Computing Science, Poznan University of Technology , 60-965 Poznan, Poland"},{"name":"Institute of Bioorganic Chemistry, Polish Academy of Sciences , 61-704 Poznan, Poland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8724-7908","authenticated-orcid":false,"given":"Marta","family":"Szachniuk","sequence":"additional","affiliation":[{"name":"Institute of Computing Science, Poznan University of Technology , 60-965 Poznan, Poland"},{"name":"Institute of Bioorganic Chemistry, Polish Academy of Sciences , 61-704 Poznan, Poland"}]}],"member":"286","published-online":{"date-parts":[[2022,6,8]]},"reference":[{"key":"2023041405371602900_","doi-asserted-by":"crossref","first-page":"1218","DOI":"10.1093\/bioinformatics\/btaa944","article-title":"RNANet: an automatically built dual-source dataset integrating homologous sequences and RNA structures","volume":"37","author":"Becquey","year":"2021","journal-title":"Bioinformatics"},{"key":"2023041405371602900_","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"2023041405371602900_","doi-asserted-by":"crossref","first-page":"250","DOI":"10.1261\/rna.078685.121","article-title":"Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions","volume":"28","author":"Carrascoza","year":"2022","journal-title":"RNA"},{"key":"2023041405371602900_","first-page":"281","volume-title":"Nucleic Acids and Molecular Biology","author":"Leontis","year":"2012"},{"key":"2023041405371602900_","first-page":"576","article-title":"RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools","volume":"48","author":"Magnus","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2023041405371602900_","doi-asserted-by":"crossref","first-page":"502","DOI":"10.1093\/nar\/gkg012","article-title":"RNABase: an annotated database of RNA structures","volume":"31","author":"Murthy","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"2023041405371602900_","doi-asserted-by":"crossref","first-page":"9625","DOI":"10.1093\/nar\/gkab716","article-title":"Entanglements of structure elements revealed in RNA 3D models","volume":"49","author":"Popenda","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2023041405371602900_","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1007\/s00285-007-0110-x","article-title":"FR3D: finding local and composite recurrent structural motifs in RNA 3D structures","volume":"56","author":"Sarver","year":"2008","journal-title":"J. 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