{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:56Z","timestamp":1772138096239,"version":"3.50.1"},"reference-count":58,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2019,7,26]],"date-time":"2019-07-26T00:00:00Z","timestamp":1564099200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100007225","name":"Ministry of Science and Technology","doi-asserted-by":"publisher","award":["103-2627-M-007-001"],"award-info":[{"award-number":["103-2627-M-007-001"]}],"id":[{"id":"10.13039\/100007225","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007225","name":"Ministry of Science and Technology","doi-asserted-by":"publisher","award":["104-2113-M-007-019"],"award-info":[{"award-number":["104-2113-M-007-019"]}],"id":[{"id":"10.13039\/100007225","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Quaternary structure determination for transmembrane\/soluble proteins requires a reliable computational protocol that leverages observed distance restraints and\/or cyclic symmetry (Cn symmetry) found in most homo-oligomeric transmembrane proteins.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We survey 118 X-ray crystallographically solved structures of homo-oligomeric transmembrane proteins (HoTPs) and find that \u223c97% are Cn symmetric. Given the prevalence of Cn symmetric HoTPs and the benefits of incorporating geometry restraints in aiding quaternary structure determination, we introduce two new filters, the distance-restraints (DR) and the Symmetry-Imposed Packing (SIP) filters. SIP relies on a new method that can rebuild the closest ideal Cn symmetric complex from docking poses containing a homo-dimer without prior knowledge of the number (n) of monomers. Using only the geometrical filter, SIP, near-native poses of 7 HoTPs in their monomeric states can be correctly identified in the top-10 for 71% of all cases, or 29% among 31 HoTP structures obtained through homology modeling, while ZDOCK alone returns 14 and 3%, respectively. When the n is given, the optional n-mer filter is applied with SIP and returns the near-native poses for 76% of the test set within the top-10, outperforming M-ZDOCK\u2019s 55% and Sam\u2019s 47%. While applying only SIP to three HoTPs that comes with distance restraints, we found the near-native poses were ranked 1st, 1st and 10th among 54 000 possible decoys. The results are further improved to 1st, 1st and 3rd when both DR and SIP filters are used. By applying only DR, a soluble system with distance restraints is recovered at the 1st-ranked pose.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>https:\/\/github.com\/capslockwizard\/drsip.<\/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\/btz579","type":"journal-article","created":{"date-parts":[[2019,7,24]],"date-time":"2019-07-24T07:27:00Z","timestamp":1563953220000},"page":"449-461","source":"Crossref","is-referenced-by-count":2,"title":["DR-SIP: protocols for higher order structure modeling with distance restraints- and cyclic symmetry-imposed packing"],"prefix":"10.1093","volume":"36","author":[{"given":"Justin","family":"Chan","sequence":"first","affiliation":[{"name":"Institute of Bioinformatics and Structural Biology, National Tsing Hua University , Hsinchu, Taiwan"},{"name":"Bioinformatics Program, Taiwan International Graduate Program , Institute of Information Sciences, Academia Sinica, Taipei, Taiwan"}]},{"given":"Jinhao","family":"Zou","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics and Structural Biology, National Tsing Hua University , Hsinchu, Taiwan"},{"name":"UTHealth Graduate School of Biomedical Science, University of Texas MD Anderson Cancer Center , Houston, TX 77030, USA"}]},{"given":"Christopher Llynard","family":"Ortiz","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics and Structural Biology, National Tsing Hua University , Hsinchu, Taiwan"}]},{"given":"Chi-Hong","family":"Chang Chien","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics and Structural Biology, National Tsing Hua University , Hsinchu, Taiwan"}]},{"given":"Rong-Long","family":"Pan","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics and Structural Biology, National Tsing Hua University , Hsinchu, Taiwan"}]},{"given":"Lee-Wei","family":"Yang","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics and Structural Biology, National Tsing Hua University , Hsinchu, Taiwan"},{"name":"Bioinformatics Program, Taiwan International Graduate Program , Institute of Information Sciences, Academia Sinica, Taipei, Taiwan"},{"name":"Physics Division, National Center for Theoretical Sciences , National Tsing Hua University, Hsinchu, Taiwan"}]}],"member":"286","published-online":{"date-parts":[[2019,7,26]]},"reference":[{"key":"2023013112081417700_btz579-B1","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1146\/annurev.biochem.77.060407.135530","article-title":"Integrating diverse data for structure determination of macromolecular assemblies","volume":"77","author":"Alber","year":"2008","journal-title":"Annu. 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