{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,5]],"date-time":"2026-07-05T03:12:07Z","timestamp":1783221127064,"version":"3.54.6"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"23","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Protein residue\u2013residue contacts continue to play a larger and larger role in protein tertiary structure modeling and evaluation. Yet, while the importance of contact information increases, the performance of sequence-based contact predictors has improved slowly. New approaches and methods are needed to spur further development and progress in the field.<\/jats:p>\n               <jats:p>Results: Here we present DNCON, a new sequence-based residue\u2013residue contact predictor using deep networks and boosting techniques. Making use of graphical processing units and CUDA parallel computing technology, we are able to train large boosted ensembles of residue\u2013residue contact predictors achieving state-of-the-art performance.<\/jats:p>\n               <jats:p>Availability: The web server of the prediction method (DNCON) is available at http:\/\/iris.rnet.missouri.edu\/dncon\/.<\/jats:p>\n               <jats:p>Contact: \u00a0chengji@missouri.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts598","type":"journal-article","created":{"date-parts":[[2012,10,10]],"date-time":"2012-10-10T08:45:27Z","timestamp":1349858727000},"page":"3066-3072","source":"Crossref","is-referenced-by-count":145,"title":["Predicting protein residue\u2013residue contacts using deep networks and boosting"],"prefix":"10.1093","volume":"28","author":[{"given":"Jesse","family":"Eickholt","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianlin","family":"Cheng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2012,10,9]]},"reference":[{"key":"2023062411491685300_bts598-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":"2023062411491685300_bts598-B2","doi-asserted-by":"crossref","first-page":"6395","DOI":"10.1073\/pnas.0408677102","article-title":"Solving the protein sequence metric problem","volume":"102","author":"Atchley","year":"2005","journal-title":"Proc. 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