{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,20]],"date-time":"2025-10-20T10:12:41Z","timestamp":1760955161863},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2552,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The recent development of methods for modeling RNA 3D structures using coarse-grain approaches creates a need to bridge low- and high-resolution modeling methods. Although they contain topological information, coarse-grain models lack atomic detail, which limits their utility for some applications.<\/jats:p>\n               <jats:p>Results: We have developed a method for adding full atomic detail to coarse-grain models of RNA 3D structures. Our method [Coarse to Atomic (C2A)] uses geometries observed in known RNA crystal structures. Our method rebuilds full atomic detail from ideal coarse-grain backbones taken from crystal structures to within 1.87\u20133.31 \u00c5 RMSD of the full atomic crystal structure. When starting from coarse-grain models generated by the modeling tool NAST, our method builds full atomic structures that are within 1.00 \u00c5 RMSD of the starting structure. The resulting full atomic structures can be used as starting points for higher resolution modeling, thus bridging high- and low-resolution approaches to modeling RNA 3D structure.<\/jats:p>\n               <jats:p>Availability: Code for the C2A method, as well as the examples discussed in this article, are freely available at www.simtk.org\/home\/c2a.<\/jats:p>\n               <jats:p>Contact: \u00a0russ.altman@stanford.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp576","type":"journal-article","created":{"date-parts":[[2009,10,8]],"date-time":"2009-10-08T00:34:41Z","timestamp":1254962081000},"page":"3259-3266","source":"Crossref","is-referenced-by-count":50,"title":["Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models"],"prefix":"10.1093","volume":"25","author":[{"given":"Magdalena A.","family":"Jonikas","sequence":"first","affiliation":[{"name":"1 Department of Bioengineering and 2Department of Genetics, Stanford University, Stanford, CA 94305, USA"}]},{"given":"Randall J.","family":"Radmer","sequence":"additional","affiliation":[{"name":"1 Department of Bioengineering and 2Department of Genetics, Stanford University, Stanford, CA 94305, USA"}]},{"given":"Russ B.","family":"Altman","sequence":"additional","affiliation":[{"name":"1 Department of Bioengineering and 2Department of Genetics, Stanford University, Stanford, CA 94305, USA"},{"name":"1 Department of Bioengineering and 2Department of Genetics, Stanford University, Stanford, CA 94305, USA"}]}],"member":"286","published-online":{"date-parts":[[2009,10,7]]},"reference":[{"key":"2023013112144153200_B1","doi-asserted-by":"crossref","DOI":"10.1126\/science.289.5481.905","article-title":"The complete atomic structure of the large ribosomal subunit at 2.4 a resolution","volume":"289","author":"Ban","year":"2000","journal-title":"Science"},{"key":"2023013112144153200_B2","doi-asserted-by":"crossref","first-page":"1678","DOI":"10.1126\/science.273.5282.1678","article-title":"Crystal structure of a group I ribozyme domain: principles of RNA packing","volume":"273","author":"Cate","year":"1996","journal-title":"Science"},{"key":"2023013112144153200_B3","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1021\/ja952883d","article-title":"Geometric parameters in nucleic acids: nitrogenous bases","volume":"118","author":"Clowney","year":"1996","journal-title":"J. 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