{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T14:24:07Z","timestamp":1772202247362,"version":"3.50.1"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The prediction of a protein\u2019s contact map has become in recent years, a crucial stepping stone for the prediction of the complete 3D structure of a protein. In this article, we describe a methodology for this problem that was shown to be successful in CASP8 and CASP9. The methodology is based on (i) the fusion of the prediction of a variety of structural aspects of protein residues, (ii) an ensemble strategy used to facilitate the training process and (iii) a rule-based machine learning system from which we can extract human-readable explanations of the predictor and derive useful information about the contact map representation.<\/jats:p>\n               <jats:p>Results: The main part of the evaluation is the comparison against the sequence-based contact prediction methods from CASP9, where our method presented the best rank in five out of the six evaluated metrics. We also assess the impact of the size of the ensemble used in our predictor to show the trade-off between performance and training time of our method. Finally, we also study the rule sets generated by our machine learning system. From this analysis, we are able to estimate the contribution of the attributes in our representation and how these interact to derive contact predictions.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/icos.cs.nott.ac.uk\/servers\/psp.html.<\/jats:p>\n               <jats:p>Contact: \u00a0natalio.krasnogor@nottingham.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts472","type":"journal-article","created":{"date-parts":[[2012,7,26]],"date-time":"2012-07-26T03:24:31Z","timestamp":1343273071000},"page":"2441-2448","source":"Crossref","is-referenced-by-count":38,"title":["Contact map prediction using a large-scale ensemble of rule sets and the fusion of multiple predicted structural features"],"prefix":"10.1093","volume":"28","author":[{"given":"Jaume","family":"Bacardit","sequence":"first","affiliation":[{"name":"1 Interdisciplinary Computing and Complex Systems (ICOS) research group, School of Computer Science, University of Nottingham, Nottingham, NG8 1BB, UK and 2School of Engineering, Pablo de Olavide University, Sevilla, 41013, Spain"}]},{"given":"Pawe\u0142","family":"Widera","sequence":"additional","affiliation":[{"name":"1 Interdisciplinary Computing and Complex Systems (ICOS) research group, School of Computer Science, University of Nottingham, Nottingham, NG8 1BB, UK and 2School of Engineering, Pablo de Olavide University, Sevilla, 41013, Spain"}]},{"given":"Alfonso","family":"M\u00e1rquez-Chamorro","sequence":"additional","affiliation":[{"name":"1 Interdisciplinary Computing and Complex Systems (ICOS) research group, School of Computer Science, University of Nottingham, Nottingham, NG8 1BB, UK and 2School of Engineering, Pablo de Olavide University, Sevilla, 41013, Spain"}]},{"given":"Federico","family":"Divina","sequence":"additional","affiliation":[{"name":"1 Interdisciplinary Computing and Complex Systems (ICOS) research group, School of Computer Science, University of Nottingham, Nottingham, NG8 1BB, UK and 2School of Engineering, Pablo de Olavide University, Sevilla, 41013, Spain"}]},{"given":"Jes\u00fas S.","family":"Aguilar-Ruiz","sequence":"additional","affiliation":[{"name":"1 Interdisciplinary Computing and Complex Systems (ICOS) research group, School of Computer Science, University of Nottingham, Nottingham, NG8 1BB, UK and 2School of Engineering, Pablo de Olavide University, Sevilla, 41013, Spain"}]},{"given":"Natalio","family":"Krasnogor","sequence":"additional","affiliation":[{"name":"1 Interdisciplinary Computing and Complex Systems (ICOS) research group, School of Computer Science, University of Nottingham, Nottingham, NG8 1BB, UK and 2School of Engineering, Pablo de Olavide University, Sevilla, 41013, Spain"}]}],"member":"286","published-online":{"date-parts":[[2012,7,25]]},"reference":[{"key":"2023012513061649700_bts472-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":"2023012513061649700_bts472-B2","doi-asserted-by":"crossref","first-page":"pp. 247","DOI":"10.1145\/1143997.1144041","article-title":"Coordination number prediction using learning classifier systems: performance and interpretability","author":"Bacardit","year":"2006","journal-title":"In GECCO \u201906: Proceedings of the 8th annual conference on Genetic and evolutionary computation"},{"key":"2023012513061649700_bts472-B3","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/1471-2105-10-6","article-title":"Automated alphabet reduction for protein datasets","volume":"10","author":"Bacardit","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023012513061649700_bts472-B4","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1007\/s12293-008-0005-4","article-title":"Improving the scalability of rule-based evolutionary learning","volume":"1","author":"Bacardit","year":"2009","journal-title":"Memetic Comput."},{"key":"2023012513061649700_bts472-B5","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1145\/235815.235821","article-title":"The quickhull algorithm for convex hulls","volume":"22","author":"Barber","year":"1996","journal-title":"ACM T. 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