{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T00:20:42Z","timestamp":1778631642789,"version":"3.51.4"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"24","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2005,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Summary: Predicting disulfide connectivity precisely helps towards the solution of protein structure prediction. In this study, a descriptor derived from the sequential distance between oxidized cysteines (denoted as DOC) is proposed. An approach using support vector machine (SVM) method based on weighted graph matching was further developed to predict the disulfide connectivity pattern in proteins. When DOC was applied, prediction accuracy of 63% for our SVM models could be achieved, which is significantly higher than those obtained from previous approaches. The results show that using the non-local descriptor DOC coupled with local sequence profiles significantly improves the prediction accuracy. These improvements demonstrate that DOC, with a proper scaling scheme, is an effective feature for the prediction of disulfide connectivity. The method developed in this work is available at the web server PreCys (prediction of cys\u2013cys linkages of proteins).<\/jats:p><jats:p>Availability: \u00a0<\/jats:p><jats:p>Contact: \u00a0cykao@csie.ntu.edu.tw<\/jats:p><jats:p>Supplementary information: Supplementary data, detailed results, tables and information are available at<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti715","type":"journal-article","created":{"date-parts":[[2005,10,14]],"date-time":"2005-10-14T00:24:37Z","timestamp":1129249477000},"page":"4416-4419","source":"Crossref","is-referenced-by-count":34,"title":["Improving disulfide connectivity prediction with sequential distance between oxidized cysteines"],"prefix":"10.1093","volume":"21","author":[{"given":"Chi-Hung","family":"Tsai","sequence":"first","affiliation":[{"name":"Department of Computer Science and Information Engineering, National Taiwan University 1 \u00a0 1 \u00a0 \u00a0 Taipei, Taiwan 106"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bo-Juen","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Information Engineering, National Taiwan University 1 \u00a0 1 \u00a0 \u00a0 Taipei, Taiwan 106"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chen-hsiung","family":"Chan","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Information Engineering, National Taiwan University 1 \u00a0 1 \u00a0 \u00a0 Taipei, Taiwan 106"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hsuan-Liang","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Chemical Engineering and Graduate Institute of Biotechnology, National Taipei University of Technology 2 \u00a0 2 \u00a0 \u00a0 Taipei, Taiwan 10608"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cheng-Yan","family":"Kao","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Information Engineering, National Taiwan University 1 \u00a0 1 \u00a0 \u00a0 Taipei, Taiwan 106"},{"name":"Institute for Information Industry 3 \u00a0 3 \u00a0 \u00a0 Taipei, Taiwan 106"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2005,10,13]]},"reference":[{"key":"2023061007325520000_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":"2023061007325520000_b2","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1093\/nar\/28.1.45","article-title":"The Swiss\u2013Prot protein sequence database and its supplement TrEMBL in 2000","volume":"28","author":"Bairoch","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2023061007325520000_b3","first-page":"97","article-title":"Large-scale prediction of disulphide bond connectivity","volume-title":"Advances in Neural Information Processing Systems 17","author":"Baldi","year":"2005"},{"key":"2023061007325520000_b4","article-title":"LIBSVM: introduction and benchmarks","volume-title":"Technical Report","author":"Chang","year":"2000"},{"key":"2023061007325520000_b5","doi-asserted-by":"crossref","first-page":"957","DOI":"10.1093\/bioinformatics\/17.10.957","article-title":"Prediction of disulfide connectivity in proteins","volume":"17","author":"Fariselli","year":"2001","journal-title":"Bioinformatics"},{"key":"2023061007325520000_b6","first-page":"464","article-title":"A neural network based method for predicting the disulfide connectivity in proteins","volume-title":"Knowledge based intelligent information engineering systems and allied technologies (KES 2002)","author":"Fariselli","year":"2002"},{"key":"2023061007325520000_b7","doi-asserted-by":"crossref","first-page":"2336","DOI":"10.1093\/bioinformatics\/bti328","article-title":"Disulfide connectivity prediction using secondary structure information and diresidue frequencies","volume":"21","author":"Ferr\u00e8","year":"2005","journal-title":"Bioinformatics"},{"key":"2023061007325520000_b8","unstructured":"Gabow H.N. 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