{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T07:48:10Z","timestamp":1774943290935,"version":"3.50.1"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2017,12,21]],"date-time":"2017-12-21T00:00:00Z","timestamp":1513814400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"NSF","doi-asserted-by":"publisher","award":["11501306, 11501407"],"award-info":[{"award-number":["11501306, 11501407"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["GM083107 and GM116960"],"award-info":[{"award-number":["GM083107 and GM116960"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DBI1564756"],"award-info":[{"award-number":["DBI1564756"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>As protein structure is more conserved than sequence during evolution, multiple structure alignment can be more informative than multiple sequence alignment, especially for distantly related proteins. With the rapid increase of the number of protein structures in the Protein Data Bank, it becomes urgent to develop efficient algorithms for multiple structure alignment.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>A new multiple structure alignment algorithm (mTM-align) was proposed, which is an extension of the highly efficient pairwise structure alignment program TM-align. The algorithm was benchmarked on four widely used datasets, HOMSTRAD, SABmark_sup, SABmark_twi and SISY-multiple, showing that mTM-align consistently outperforms other algorithms. In addition, the comparison with the manually curated alignments in the HOMSTRAD database shows that the automated alignments built by mTM-align are in general more accurate. Therefore, mTM-align may be used as a reliable complement to construct multiple structure alignments for real-world applications.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>http:\/\/yanglab.nankai.edu.cn\/mTM-align<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx828","type":"journal-article","created":{"date-parts":[[2017,12,20]],"date-time":"2017-12-20T22:03:02Z","timestamp":1513807382000},"page":"1719-1725","source":"Crossref","is-referenced-by-count":134,"title":["mTM-align: an algorithm for fast and accurate multiple protein structure alignment"],"prefix":"10.1093","volume":"34","author":[{"given":"Runze","family":"Dong","sequence":"first","affiliation":[{"name":"School of Mathematical Sciences, Nankai University, Tianjin, China"}]},{"given":"Zhenling","family":"Peng","sequence":"additional","affiliation":[{"name":"Center for Applied Mathematics, Tianjin University, Tianjin, China"}]},{"given":"Yang","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2912-7737","authenticated-orcid":false,"given":"Jianyi","family":"Yang","sequence":"additional","affiliation":[{"name":"School of Mathematical Sciences, Nankai University, Tianjin, China"}]}],"member":"286","published-online":{"date-parts":[[2017,12,21]]},"reference":[{"key":"2023012810010976700_btx828-B1","doi-asserted-by":"crossref","first-page":"2027","DOI":"10.1002\/pro.213","article-title":"Accuracy analysis of multiple structure alignments","volume":"18","author":"Berbalk","year":"2009","journal-title":"Protein Sci"},{"key":"2023012810010976700_btx828-B2","doi-asserted-by":"crossref","first-page":"1080","DOI":"10.1093\/bioinformatics\/btl046","article-title":"Development and validation of a consistency based multiple structure alignment algorithm","volume":"22","author":"Ebert","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012810010976700_btx828-B3","doi-asserted-by":"crossref","first-page":"W100","DOI":"10.1093\/nar\/gkh464","article-title":"CE-MC: a multiple protein structure alignment server","volume":"32","author":"Guda","year":"2004","journal-title":"Nucl. 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