{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T07:52:37Z","timestamp":1778053957241,"version":"3.51.4"},"reference-count":60,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2017,1,16]],"date-time":"2017-01-16T00:00:00Z","timestamp":1484524800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000266","name":"Engineering and Physical Sciences Research Council","doi-asserted-by":"publisher","award":["EP\/G037280\/1"],"award-info":[{"award-number":["EP\/G037280\/1"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]},{"name":"UCB Pharma Ltd and Roche"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Loops are often vital for protein function, however, their irregular structures make them difficult to model accurately. Current loop modelling algorithms can mostly be divided into two categories: knowledge-based, where databases of fragments are searched to find suitable conformations and ab initio, where conformations are generated computationally. Existing knowledge-based methods only use fragments that are the same length as the target, even though loops of slightly different lengths may adopt similar conformations. Here, we present a novel method, Sphinx, which combines ab initio techniques with the potential extra structural information contained within loops of a different length to improve structure prediction.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We show that Sphinx is able to generate high-accuracy predictions and decoy sets enriched with near-native loop conformations, performing better than the ab initio algorithm on which it is based. In addition, it is able to provide predictions for every target, unlike some knowledge-based methods. Sphinx can be used successfully for the difficult problem of antibody H3 prediction, outperforming RosettaAntibody, one of the leading H3-specific ab initio methods, both in accuracy and speed.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and Implementation<\/jats:title><jats:p>Sphinx is available at http:\/\/opig.stats.ox.ac.uk\/webapps\/sphinx.<\/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\/btw823","type":"journal-article","created":{"date-parts":[[2017,1,17]],"date-time":"2017-01-17T01:43:51Z","timestamp":1484617431000},"page":"1346-1353","source":"Crossref","is-referenced-by-count":48,"title":["Sphinx: merging knowledge-based and<i>ab initio<\/i>approaches to improve protein loop prediction"],"prefix":"10.1093","volume":"33","author":[{"given":"Claire","family":"Marks","sequence":"first","affiliation":[{"name":"Department of Statistics, University of Oxford, Oxford, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jaroslaw","family":"Nowak","sequence":"additional","affiliation":[{"name":"Department of Statistics, University of Oxford, Oxford, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stefan","family":"Klostermann","sequence":"additional","affiliation":[{"name":"Pharma Research and Early Development, Informatics, Roche Innovation Center Munich, Penzberg, DE, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guy","family":"Georges","sequence":"additional","affiliation":[{"name":"Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, DE, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James","family":"Dunbar","sequence":"additional","affiliation":[{"name":"Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, DE, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiye","family":"Shi","sequence":"additional","affiliation":[{"name":"Department of Informatics, UCB Pharma, Slough, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sebastian","family":"Kelm","sequence":"additional","affiliation":[{"name":"Department of Informatics, UCB Pharma, Slough, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Charlotte M","family":"Deane","sequence":"additional","affiliation":[{"name":"Department of Statistics, University of Oxford, Oxford, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,1,16]]},"reference":[{"key":"2023020205015144900_btw823-B1","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1146\/annurev.iy.06.040188.003011","article-title":"Three-dimensional structure of antibodies","volume":"6","author":"Alzari","year":"1998","journal-title":"Annu. 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