{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,13]],"date-time":"2026-04-13T22:45:31Z","timestamp":1776120331467,"version":"3.50.1"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"16","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Disulfide bonds stabilize protein structures and play relevant roles in their functions. Their formation requires an oxidizing environment and their stability is consequently depending on the redox ambient potential, which may differ according to the subcellular compartment. Several methods are available to predict cysteine-bonding state and connectivity patterns. However, none of them takes into consideration the relevance of protein subcellular localization.<\/jats:p><jats:p>Results: Here we develop DISLOCATE, a two-step method based on machine learning models for predicting both the bonding state and the connectivity patterns of cysteine residues in a protein chain. We find that the inclusion of protein subcellular localization improves the performance of these predictive steps by 3 and 2 percentage points, respectively. When compared with previously developed methods for predicting disulfide bonds from sequence, DISLOCATE improves the overall performance by more than 10 percentage points.<\/jats:p><jats:p>Availability: The method and the dataset are available at the Web page http:\/\/www.biocomp.unibo.it\/savojard\/Dislocate.html. GRHCRF code is available at http:\/\/www.biocomp.unibo.it\/savojard\/biocrf.html.<\/jats:p><jats:p>Contact: \u00a0piero.fariselli@unibo.it<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr387","type":"journal-article","created":{"date-parts":[[2011,6,30]],"date-time":"2011-06-30T00:57:23Z","timestamp":1309395443000},"page":"2224-2230","source":"Crossref","is-referenced-by-count":38,"title":["Improving the prediction of disulfide bonds in Eukaryotes with machine learning methods and protein subcellular localization"],"prefix":"10.1093","volume":"27","author":[{"given":"Castrense","family":"Savojardo","sequence":"first","affiliation":[{"name":"1 Biocomputing Group, University of Bologna, CIRI-Life Science and Health Technologies and Department of Biology, Via San Giacomo 9\/2, Bologna, 2Department of Computer Science, Via Mura Anteo Zamboni 7, 40127 Bologna and 3Externautics s.p.a., Department of Bioinformatics, Via Fiorentina 1, 53100 Siena, Italy"},{"name":"1 Biocomputing Group, University of Bologna, CIRI-Life Science and Health Technologies and Department of Biology, Via San Giacomo 9\/2, Bologna, 2Department of Computer Science, Via Mura Anteo Zamboni 7, 40127 Bologna and 3Externautics s.p.a., Department of Bioinformatics, Via Fiorentina 1, 53100 Siena, Italy"}]},{"given":"Piero","family":"Fariselli","sequence":"additional","affiliation":[{"name":"1 Biocomputing Group, University of Bologna, CIRI-Life Science and Health Technologies and Department of Biology, Via San Giacomo 9\/2, Bologna, 2Department of Computer Science, Via Mura Anteo Zamboni 7, 40127 Bologna and 3Externautics s.p.a., Department of Bioinformatics, Via Fiorentina 1, 53100 Siena, Italy"},{"name":"1 Biocomputing Group, University of Bologna, CIRI-Life Science and Health Technologies and Department of Biology, Via San Giacomo 9\/2, Bologna, 2Department of Computer Science, Via Mura Anteo Zamboni 7, 40127 Bologna and 3Externautics s.p.a., Department of Bioinformatics, Via Fiorentina 1, 53100 Siena, Italy"}]},{"given":"Monther","family":"Alhamdoosh","sequence":"additional","affiliation":[{"name":"1 Biocomputing Group, University of Bologna, CIRI-Life Science and Health Technologies and Department of Biology, Via San Giacomo 9\/2, Bologna, 2Department of Computer Science, Via Mura Anteo Zamboni 7, 40127 Bologna and 3Externautics s.p.a., Department of Bioinformatics, Via Fiorentina 1, 53100 Siena, Italy"}]},{"given":"Pier Luigi","family":"Martelli","sequence":"additional","affiliation":[{"name":"1 Biocomputing Group, University of Bologna, CIRI-Life Science and Health Technologies and Department of Biology, Via San Giacomo 9\/2, Bologna, 2Department of Computer Science, Via Mura Anteo Zamboni 7, 40127 Bologna and 3Externautics s.p.a., Department of Bioinformatics, Via Fiorentina 1, 53100 Siena, Italy"}]},{"given":"Andrea","family":"Pierleoni","sequence":"additional","affiliation":[{"name":"1 Biocomputing Group, University of Bologna, CIRI-Life Science and Health Technologies and Department of Biology, Via San Giacomo 9\/2, Bologna, 2Department of Computer Science, Via Mura Anteo Zamboni 7, 40127 Bologna and 3Externautics s.p.a., Department of Bioinformatics, Via Fiorentina 1, 53100 Siena, Italy"}]},{"given":"Rita","family":"Casadio","sequence":"additional","affiliation":[{"name":"1 Biocomputing Group, University of Bologna, CIRI-Life Science and Health Technologies and Department of Biology, Via San Giacomo 9\/2, Bologna, 2Department of Computer Science, Via Mura Anteo Zamboni 7, 40127 Bologna and 3Externautics s.p.a., Department of Bioinformatics, Via Fiorentina 1, 53100 Siena, Italy"}]}],"member":"286","published-online":{"date-parts":[[2011,6,29]]},"reference":[{"key":"2023012511514529700_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":"2023012511514529700_B2","doi-asserted-by":"crossref","first-page":"1190","DOI":"10.1137\/0916069","article-title":"A limited memory algorithm for bound constrained optimization","volume":"16","author":"Byrd","year":"1995","journal-title":"SIAM J. 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