{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T07:51:46Z","timestamp":1778053906634,"version":"3.51.4"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Membrane proteins are clinically relevant, yet their crystal structures are rare. Models of membrane proteins are typically built from template structures with low sequence identity to the target sequence, using a sequence-structure alignment as a blueprint. This alignment is usually made with programs designed for use on soluble proteins. Biological membranes have layers of varying hydrophobicity, and membrane proteins have different amino-acid substitution preferences from their soluble counterparts. Here we include these factors into an alignment method to improve alignments and consequently improve membrane protein models.<\/jats:p>\n               <jats:p>Results: We developed Membrane Protein Threader (MP-T), a sequence-structure alignment tool for membrane proteins based on multiple sequence alignment. Alignment accuracy is tested against seven other alignment methods over 165 non-redundant alignments of membrane proteins. MP-T produces more accurate alignments than all other methods tested (\u03b4FM from +0.9 to +5.5%). Alignments generated by MP-T also lead to significantly better models than those of the best alternative alignment tool (one-fourth of models see an increase in GDT_TS of \u22654%).<\/jats:p>\n               <jats:p>Availability: All source code, alignments and models are available at http:\/\/www.stats.ox.ac.uk\/proteins\/resources<\/jats:p>\n               <jats:p>Contact: \u00a0deane@stats.ox.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts640","type":"journal-article","created":{"date-parts":[[2012,10,31]],"date-time":"2012-10-31T04:41:41Z","timestamp":1351658501000},"page":"54-61","source":"Crossref","is-referenced-by-count":29,"title":["MP-T: improving membrane protein alignment for structure prediction"],"prefix":"10.1093","volume":"29","author":[{"given":"Jamie R.","family":"Hill","sequence":"first","affiliation":[{"name":"Department of Statistics, University of Oxford, Oxford, OX1 3TG, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Charlotte M.","family":"Deane","sequence":"additional","affiliation":[{"name":"Department of Statistics, University of Oxford, Oxford, OX1 3TG, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,10,30]]},"reference":[{"key":"2023020303304354100_bts640-B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023020303304354100_bts640-B2","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The protein data bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2023020303304354100_bts640-B3","doi-asserted-by":"crossref","first-page":"S1","DOI":"10.1186\/1471-2105-13-S4-S1","article-title":"Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee","volume":"13","author":"Chang","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"2023020303304354100_bts640-B4","doi-asserted-by":"crossref","first-page":"1431","DOI":"10.1002\/prot.22658","article-title":"FREAD revisited: accurate loop structure prediction using a database search algorithm","volume":"78","author":"Choi","year":"2010","journal-title":"Proteins"},{"key":"2023020303304354100_bts640-B5","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MU SCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023020303304354100_bts640-B6","doi-asserted-by":"crossref","first-page":"2460","DOI":"10.1093\/bioinformatics\/btq461","article-title":"Search and clustering orders of magnitude faster than BLAST","volume":"26","author":"Edgar","year":"2010","journal-title":"Bioinformatics"},{"key":"2023020303304354100_bts640-B7","doi-asserted-by":"crossref","first-page":"508","DOI":"10.1529\/biophysj.106.082313","article-title":"On the accuracy of homology modeling and sequence alignment methods applied to membrane proteins","volume":"91","author":"Forrest","year":"2006","journal-title":"Biophys. 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