{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T21:23:10Z","timestamp":1785273790444,"version":"3.55.0"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2016,10,1]],"date-time":"2016-10-01T00:00:00Z","timestamp":1475280000000},"content-version":"vor","delay-in-days":675,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Motivation: Recent developments of statistical techniques to infer direct evolutionary couplings between residue pairs have rendered covariation-based contact prediction a viable means for accurate 3D modelling of proteins, with no information other than the sequence required. To extend the usefulness of contact prediction, we have designed a new meta-predictor (MetaPSICOV) which combines three distinct approaches for inferring covariation signals from multiple sequence alignments, considers a broad range of other sequence-derived features and, uniquely, a range of metrics which describe both the local and global quality of the input multiple sequence alignment. Finally, we use a two-stage predictor, where the second stage filters the output of the first stage. This two-stage predictor is additionally evaluated on its ability to accurately predict the long range network of hydrogen bonds, including correctly assigning the donor and acceptor residues.<\/jats:p>\n                  <jats:p>Results: Using the original PSICOV benchmark set of 150 protein families, MetaPSICOV achieves a mean precision of 0.54 for top-L predicted long range contacts\u2014around 60% higher than PSICOV, and around 40% better than CCMpred. In de novo protein structure prediction using FRAGFOLD, MetaPSICOV is able to improve the TM-scores of models by a median of 0.05 compared with PSICOV. Lastly, for predicting long range hydrogen bonding, MetaPSICOV-HB achieves a precision of 0.69 for the top-L\/10 hydrogen bonds compared with just 0.26 for the baseline MetaPSICOV.<\/jats:p>\n                  <jats:p>Availability and implementation: MetaPSICOV is available as a freely available web server at http:\/\/bioinf.cs.ucl.ac.uk\/MetaPSICOV. Raw data (predicted contact lists and 3D models) and source code can be downloaded from http:\/\/bioinf.cs.ucl.ac.uk\/downloads\/MetaPSICOV.<\/jats:p>\n                  <jats:p>Contact: \u00a0d.t.jones@ucl.ac.uk<\/jats:p>\n                  <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu791","type":"journal-article","created":{"date-parts":[[2014,11,28]],"date-time":"2014-11-28T10:35:07Z","timestamp":1417170907000},"page":"999-1006","source":"Crossref","is-referenced-by-count":325,"title":["MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins"],"prefix":"10.1093","volume":"31","author":[{"given":"David T.","family":"Jones","sequence":"first","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, University College London, London WC1E 6BT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tanya","family":"Singh","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, University College London, London WC1E 6BT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tomasz","family":"Kosciolek","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, University College London, London WC1E 6BT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stuart","family":"Tetchner","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, University College London, London WC1E 6BT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2014,11,26]]},"reference":[{"key":"2023051309144128300_btu791-B1","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1016\/0022-2836(87)90352-4","article-title":"Correlation of co-ordinated amino acid substitutions with function in viruses related to tobacco mosaic virus.","volume":"193","author":"Altschuh","year":"1987","journal-title":"J. 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