{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,12]],"date-time":"2025-11-12T13:45:02Z","timestamp":1762955102119},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"14","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Modelling the 3D structures of proteins can often be enhanced if more than one fold template is used during the modelling process. However, in many cases, this may also result in poorer model quality for a given target or alignment method. There is a need for modelling protocols that can both consistently and significantly improve 3D models and provide an indication of when models might not benefit from the use of multiple target-template alignments. Here, we investigate the use of both global and local model quality prediction scores produced by ModFOLDclust2, to improve the selection of target-template alignments for the construction of multiple-template models. Additionally, we evaluate clustering the resulting population of multi- and single-template models for the improvement of our IntFOLD-TS tertiary structure prediction method.<\/jats:p>\n               <jats:p>Results: We find that using accurate local model quality scores to guide alignment selection is the most consistent way to significantly improve models for each of the sequence to structure alignment methods tested. In addition, using accurate global model quality for re-ranking alignments, prior to selection, further improves the majority of multi-template modelling methods tested. Furthermore, subsequent clustering of the resulting population of multiple-template models significantly improves the quality of selected models compared with the previous version of our tertiary structure prediction method, IntFOLD-TS.<\/jats:p>\n               <jats:p>Availability and implementation: Source code and binaries can be freely downloaded from http:\/\/www.reading.ac.uk\/bioinf\/downloads\/.<\/jats:p>\n               <jats:p>Contact: \u00a0l.j.mcguffin@reading.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online. http:\/\/www.reading.ac.uk\/bioinf\/MTM_suppl_info.pdf<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts292","type":"journal-article","created":{"date-parts":[[2012,5,17]],"date-time":"2012-05-17T15:46:05Z","timestamp":1337269565000},"page":"1851-1857","source":"Crossref","is-referenced-by-count":41,"title":["Improvement of 3D protein models using multiple templates guided by single-template model quality assessment"],"prefix":"10.1093","volume":"28","author":[{"given":"Maria T.","family":"Buenavista","sequence":"first","affiliation":[{"name":"1 School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AS, 2Biocomputing Section, MRC Harwell, Harwell Oxford Campus, Didcot OX11 0RD and 3Diamond Light Source, Beamline B23, Chilton, Didcot OX11 0DE, UK"},{"name":"1 School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AS, 2Biocomputing Section, MRC Harwell, Harwell Oxford Campus, Didcot OX11 0RD and 3Diamond Light Source, Beamline B23, Chilton, Didcot OX11 0DE, UK"},{"name":"1 School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AS, 2Biocomputing Section, MRC Harwell, Harwell Oxford Campus, Didcot OX11 0RD and 3Diamond Light Source, Beamline B23, Chilton, Didcot OX11 0DE, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel B.","family":"Roche","sequence":"additional","affiliation":[{"name":"1 School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AS, 2Biocomputing Section, MRC Harwell, Harwell Oxford Campus, Didcot OX11 0RD and 3Diamond Light Source, Beamline B23, Chilton, Didcot OX11 0DE, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Liam J.","family":"McGuffin","sequence":"additional","affiliation":[{"name":"1 School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AS, 2Biocomputing Section, MRC Harwell, Harwell Oxford Campus, Didcot OX11 0RD and 3Diamond Light Source, Beamline B23, Chilton, Didcot OX11 0DE, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,5,15]]},"reference":[{"key":"2023012512431336300_B1","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1186\/1472-6807-8-31","article-title":"Systematic analysis of the effect of multiple templates on the accuracy of comparative models of protein structure","volume":"8","author":"Chakravarty","year":"2008","journal-title":"BMC. 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