{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,14]],"date-time":"2026-07-14T20:45:32Z","timestamp":1784061932583,"version":"3.55.0"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2022,4,6]],"date-time":"2022-04-06T00:00:00Z","timestamp":1649203200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Gruber Science Foundation"},{"DOI":"10.13039\/100000011","name":"Howard Hughes Medical Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000011","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000051","name":"National Human Genome Research Institute","doi-asserted-by":"publisher","award":["HG011868"],"award-info":[{"award-number":["HG011868"]}],"id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,5,13]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The full description of nucleic acid conformation involves eight torsion angles per nucleotide. To simplify this description, we previously developed a representation of the nucleic acid backbone that assigns each nucleotide a pair of pseudo-torsion angles (eta and theta defined by P and C4\u02b9 atoms; or eta\u02b9 and theta\u02b9 defined by P and C1\u02b9 atoms). A Java program, AMIGOS II, is currently available for calculating eta and theta angles for RNA and for performing motif searches based on eta and theta angles. However, AMIGOS II lacks the ability to parse DNA structures and to calculate eta\u02b9 and theta\u02b9 angles. It also has little visualization capacity for 3D structure, making it difficult for users to interpret the computational results.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present AMIGOS III, a PyMOL plugin that calculates the pseudo-torsion angles eta, theta, eta\u02b9 and theta\u02b9 for both DNA and RNA structures and performs motif searching based on these angles. Compared to AMIGOS II, AMIGOS III offers improved pseudo-torsion angle visualization for RNA and faster nucleic acid worm database generation; it also introduces pseudo-torsion angle visualization for DNA and nucleic acid worm visualization. Its integration into PyMOL enables easy preparation of tertiary structure inputs and intuitive visualization of involved structures.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/pylelab\/AMIGOSIII.<\/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\/btac207","type":"journal-article","created":{"date-parts":[[2022,4,6]],"date-time":"2022-04-06T13:43:53Z","timestamp":1649252633000},"page":"2937-2939","source":"Crossref","is-referenced-by-count":7,"title":["AMIGOS III: pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8307-4210","authenticated-orcid":false,"given":"Morgan","family":"Shine","sequence":"first","affiliation":[{"name":"Yale Combined Program in the Biological and Biomedical Sciences, Yale University , New Haven, CT 06511, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7290-1324","authenticated-orcid":false,"given":"Chengxin","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Molecular, Cellular and Developmental Biology, Yale University , New Haven, CT 06511, USA"},{"name":"Department of Chemistry, Yale University , New Haven, CT 06511, USA"},{"name":"Howard Hughes Medical Institute , Chevy Chase, MD 20815, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna Marie","family":"Pyle","sequence":"additional","affiliation":[{"name":"Department of Molecular, Cellular and Developmental Biology, Yale University , New Haven, CT 06511, USA"},{"name":"Department of Chemistry, Yale University , New Haven, CT 06511, USA"},{"name":"Howard Hughes Medical Institute , Chevy Chase, MD 20815, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,4,6]]},"reference":[{"key":"2023020109150000700_btac207-B1","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1038\/nature02642","article-title":"Crystal structure of a self-splicing group I intron with both exons","volume":"430","author":"Adams","year":"2004","journal-title":"Nature"},{"key":"2023020109150000700_btac207-B2","doi-asserted-by":"crossref","first-page":"e63","DOI":"10.1093\/nar\/gkv1479","article-title":"SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction","volume":"44","author":"Boniecki","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023020109150000700_btac207-B3","doi-asserted-by":"crossref","first-page":"4882","DOI":"10.1016\/j.jmb.2016.10.015","article-title":"Identification of a GUAAY pentaloop sequence involved in a novel RNA loop-helix interaction","volume":"428","author":"Chan","year":"2016","journal-title":"J. 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