{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:24Z","timestamp":1772138064964,"version":"3.50.1"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2023,8,30]],"date-time":"2023-08-30T00:00:00Z","timestamp":1693353600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Science Center, Poland","award":["2021\/43\/D\/NZ1\/03360"],"award-info":[{"award-number":["2021\/43\/D\/NZ1\/03360"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,9,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Structure determination is a key step in the functional characterization of many non-coding RNA molecules. High-resolution RNA 3D structure determination efforts, however, are not keeping up with the pace of discovery of new non-coding RNA sequences. This increases the importance of computational approaches and low-resolution experimental data, such as from the small-angle X-ray scattering experiments. We present RNA Masonry, a computer program and a web service for a fully automated modeling of RNA 3D structures. It assemblies RNA fragments into geometrically plausible models that meet user-provided secondary structure constraints, restraints on tertiary contacts, and small-angle X-ray scattering data. We illustrate the method description with detailed benchmarks and its application to structural studies of viral RNAs with SAXS restraints.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The program web server is available at http:\/\/iimcb.genesilico.pl\/rnamasonry. The source code is available at https:\/\/gitlab.com\/gchojnowski\/rnamasonry.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad527","type":"journal-article","created":{"date-parts":[[2023,8,29]],"date-time":"2023-08-29T08:06:36Z","timestamp":1693296396000},"source":"Crossref","is-referenced-by-count":14,"title":["RNA 3D structure modeling by fragment assembly with small-angle X-ray scattering restraints"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3796-8352","authenticated-orcid":false,"given":"Grzegorz","family":"Chojnowski","sequence":"first","affiliation":[{"name":"International Institute of Molecular and Cell Biology , Warsaw 02-109, Poland"},{"name":"European Molecular Biology Laboratory, Hamburg Unit , Hamburg 22607, Germany"}]},{"given":"Rafa\u0142","family":"Zaborowski","sequence":"additional","affiliation":[{"name":"International Institute of Molecular and Cell Biology , Warsaw 02-109, Poland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5232-2234","authenticated-orcid":false,"given":"Marcin","family":"Magnus","sequence":"additional","affiliation":[{"name":"ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences , Warsaw, Poland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4361-0103","authenticated-orcid":false,"given":"Sunandan","family":"Mukherjee","sequence":"additional","affiliation":[{"name":"International Institute of Molecular and Cell Biology , Warsaw 02-109, Poland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6633-165X","authenticated-orcid":false,"given":"Janusz M","family":"Bujnicki","sequence":"additional","affiliation":[{"name":"International Institute of Molecular and Cell Biology , Warsaw 02-109, Poland"}]}],"member":"286","published-online":{"date-parts":[[2023,8,30]]},"reference":[{"key":"2023090222491403700_btad527-B1","doi-asserted-by":"crossref","first-page":"e84","DOI":"10.1093\/nar\/gkab459","article-title":"Reweighting of 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