{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T12:18:52Z","timestamp":1767961132881,"version":"3.49.0"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Motivated by the abundance, importance and unique functionality of zinc, both biologically and physiologically, we have developed an improved method for the prediction of zinc-binding sites in proteins from their amino acid sequences.<\/jats:p><jats:p>Results: By combining support vector machine (SVM) and homology-based predictions, our method predicts zinc-binding Cys, His, Asp and Glu with 75% precision (86% for Cys and His only) at 50% recall according to a 5-fold cross-validation on a non-redundant set of protein chains from the Protein Data Bank (PDB) (2727 chains, 235 of which bind zinc). Consequently, our method predicts zinc-binding Cys and His with 10% higher precision at different recall levels compared to a recently published method when tested on the same dataset.<\/jats:p><jats:p>Availability: The program is available for download at www.fos.su.se\/~nanjiang\/zincpred\/download\/<\/jats:p><jats:p>Contact: \u00a0svenh@struc.su.se<\/jats:p><jats:p>Supplementary information: All Supplementary Data can be accessed at www.fos.su.se\/~nanjiang\/zincpred\/suppliment<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm618","type":"journal-article","created":{"date-parts":[[2008,2,2]],"date-time":"2008-02-02T01:25:55Z","timestamp":1201915555000},"page":"775-782","source":"Crossref","is-referenced-by-count":103,"title":["Prediction of zinc-binding sites in proteins from sequence"],"prefix":"10.1093","volume":"24","author":[{"given":"Nanjiang","family":"Shu","sequence":"first","affiliation":[{"name":"Structural Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden"}]},{"given":"Tuping","family":"Zhou","sequence":"additional","affiliation":[{"name":"Structural Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden"}]},{"given":"Sven","family":"Hovm\u00f6ller","sequence":"additional","affiliation":[{"name":"Structural Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden"}]}],"member":"286","published-online":{"date-parts":[[2008,2,1]]},"reference":[{"key":"2023020209512466000_B1","doi-asserted-by":"crossref","first-page":"793","DOI":"10.1107\/S0907444994005263","article-title":"Refined crystal structure of liver alcohol dehydrogenase-NADH complex at 1.8 A resolution","volume":"50","author":"Al-Karadaghi","year":"1994","journal-title":"Acta Crystallogr. D Biol. Crystallogr"},{"key":"2023020209512466000_B2","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":"Nucl. Acids Res"},{"key":"2023020209512466000_B3","doi-asserted-by":"crossref","first-page":"D226","DOI":"10.1093\/nar\/gkh039","article-title":"SCOP database in 2004: refinements integrate structure and sequence family data","volume":"32","author":"Andreeva","year":"2004","journal-title":"Nucl. Acids Res"},{"key":"2023020209512466000_B4","doi-asserted-by":"crossref","first-page":"1373","DOI":"10.1093\/bioinformatics\/bth095","article-title":"A hint to search for metalloproteins in gene banks","volume":"20","author":"Andreini","year":"2004","journal-title":"Bioinformatics"},{"key":"2023020209512466000_B5","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1023\/A:1012976615056","article-title":"Zinc coordination sphere in biochemical zinc sites","volume":"14","author":"Auld","year":"2001","journal-title":"Biometals"},{"key":"2023020209512466000_B6","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1023\/A:1018332327565","article-title":"Refined solution structure of the DNA-binding domain of GAL4 and use of 3J(113Cd,1H) in structure determination","volume":"10","author":"Baleja","year":"1997","journal-title":"J. Biomol. NMR"},{"key":"2023020209512466000_B7","doi-asserted-by":"crossref","first-page":"1081","DOI":"10.1126\/science.271.5252.1081","article-title":"The galvanization of biology: a growing appreciation for the roles of zinc","volume":"271","author":"Berg","year":"1996","journal-title":"Science"},{"key":"2023020209512466000_B8","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1016\/S0022-2836(77)80200-3","article-title":"The Protein Data Bank: a computer-based archival file for macromolecular structures","volume":"112","author":"Bernstein","year":"1977","journal-title":"J. Mol. Biol"},{"key":"2023020209512466000_B9","first-page":"35","article-title":"Biological roles of ionic zinc","volume":"129","author":"Brewer","year":"1983","journal-title":"Prog. Clin. Biol. Res"},{"key":"2023020209512466000_B10","doi-asserted-by":"crossref","first-page":"897","DOI":"10.1146\/annurev.bi.61.070192.004341","article-title":"Zinc proteins: enzymes, storage proteins, transcription factors, and replication proteins","volume":"61","author":"Coleman","year":"1992","journal-title":"Annu. Rev. Biochem"},{"key":"2023020209512466000_B11","doi-asserted-by":"crossref","DOI":"10.1145\/1143844.1143874","article-title":"The relationship between Precision\u2013Recall and ROC curves","author":"Davis","year":"2006"},{"key":"2023020209512466000_B12","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1016\/j.jmb.2005.02.007","article-title":"Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions","volume":"348","author":"Ekman","year":"2005","journal-title":"J. Mol. Biol"},{"key":"2023020209512466000_B13","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1016\/S1570-9639(03)00266-8","article-title":"Nuclear magnetic resonance structures of the zinc finger domain of human DNA polymerase-alpha","volume":"1651","author":"Evanics","year":"2003","journal-title":"Biochim. Biophys. Acta"},{"key":"2023020209512466000_B14","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1093\/protein\/6.1.29","article-title":"The prediction and characterization of metal binding sites in proteins","volume":"6","author":"Gregory","year":"1993","journal-title":"Protein Eng"},{"key":"2023020209512466000_B15","doi-asserted-by":"crossref","first-page":"849","DOI":"10.1107\/S0907444904004081","article-title":"The architecture of metal coordination groups in proteins","volume":"60","author":"Harding","year":"2004","journal-title":"Acta. Crystallogr. D Biol. Crystallogr"},{"key":"2023020209512466000_B16","doi-asserted-by":"crossref","first-page":"1407","DOI":"10.1110\/ps.03589204","article-title":"The NMR solution structure of the 30S ribosomal protein S27e encoded in gene RS27_ARCFU of Archaeoglobus fulgidis reveals a novel protein fold","volume":"13","author":"Herve du Penhoat","year":"2004","journal-title":"Protein Sci"},{"key":"2023020209512466000_B17","doi-asserted-by":"crossref","first-page":"2239","DOI":"10.1021\/cr9500390","article-title":"Structural and functional aspects of metal sites in biology","volume":"96","author":"Holm","year":"1996","journal-title":"Chem. Rev"},{"key":"2023020209512466000_B18","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1006\/jmbi.1998.2163","article-title":"An evolutionary link between sporulation and prophage induction in the structure of a repressor:anti-repressor complex","volume":"283","author":"Lewis","year":"1998","journal-title":"J. Mol. Biol"},{"key":"2023020209512466000_B19","doi-asserted-by":"crossref","first-page":"1437S","DOI":"10.1093\/jn\/130.5.1437S","article-title":"Function and mechanism of zinc metalloenzymes","volume":"130","author":"McCall","year":"2000","journal-title":"J. Nutr"},{"key":"2023020209512466000_B20","volume-title":"Crystallization of Biological Macromolecules.","author":"McPherson","year":"1999"},{"key":"2023020209512466000_B21","first-page":"309","article-title":"Improving prediction of zinc binding sites by modeling the linkage between residues close in sequence","author":"Menchetti","year":"2006"},{"key":"2023020209512466000_B22","doi-asserted-by":"crossref","first-page":"3789","DOI":"10.1093\/nar\/gkg620","article-title":"UniqueProt: creating representative protein sequence sets","volume":"31","author":"Mika","year":"2003","journal-title":"Nucl. Acids Res"},{"key":"2023020209512466000_B23","doi-asserted-by":"crossref","first-page":"1531","DOI":"10.1093\/bioinformatics\/btg185","article-title":"Probabilistic scoring measures for profile-profile comparison yield more accurate short seed alignments","volume":"19","author":"Mittelman","year":"2003","journal-title":"Bioinformatics"},{"key":"2023020209512466000_B24","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1006\/jmbi.1999.2620","article-title":"Solution structure of the transactivation domain of ATF-2 comprising a zinc finger-like subdomain and a flexible subdomain","volume":"287","author":"Nagadoi","year":"1999","journal-title":"J. Mol. Biol"},{"key":"2023020209512466000_B25","first-page":"125","article-title":"Prediction of zinc finger DNA binding protein","volume":"11","author":"Nakata","year":"1995","journal-title":"Comput. Appl. Biosci"},{"key":"2023020209512466000_B26","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1186\/1471-2105-8-39","article-title":"Predicting zinc binding at the proteome level","volume":"8","author":"Passerini","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"2023020209512466000_B27","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1002\/prot.21135","article-title":"Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks","volume":"65","author":"Passerini","year":"2006","journal-title":"Proteins"},{"key":"2023020209512466000_B28","doi-asserted-by":"crossref","first-page":"586","DOI":"10.1093\/bioinformatics\/btg461","article-title":"Support vector machine classification on the web","volume":"20","author":"Pavlidis","year":"2004","journal-title":"Bioinformatics"},{"key":"2023020209512466000_B29","doi-asserted-by":"crossref","first-page":"61","DOI":"10.7551\/mitpress\/1113.003.0008","article-title":"Probabilistic outputs for support vector machines and comparison to regularized likelihood methods","volume-title":"Advances in Large Margin Classifiers.","author":"Platt","year":"2000"},{"key":"2023020209512466000_B30","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1016\/j.jmb.2004.07.019","article-title":"Predicting metal-binding site residues in low-resolution structural models","volume":"342","author":"Sodhi","year":"2004","journal-title":"J. Mol. Biol"},{"key":"2023020209512466000_B31","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s00204-005-0009-5","article-title":"Zinc: a multipurpose trace element","volume":"80","author":"Stefanidou","year":"2006","journal-title":"Arch. Toxicol"},{"key":"2023020209512466000_B32","first-page":"571","article-title":"Learning rules from highly unbalanced data sets. Data Mining, 2004","author":"Zhang","year":"2004"},{"key":"2023020209512466000_B33","doi-asserted-by":"crossref","first-page":"3986","DOI":"10.1093\/nar\/26.17.3986","article-title":"Protein sequence similarity searches using patterns as seeds","volume":"26","author":"Zhang","year":"1998","journal-title":"Nucl. Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/6\/775\/49046202\/bioinformatics_24_6_775.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/6\/775\/49046202\/bioinformatics_24_6_775.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,21]],"date-time":"2024-02-21T22:02:29Z","timestamp":1708552949000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/24\/6\/775\/192764"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,2,1]]},"references-count":33,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2008,3,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btm618","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2008,3,15]]},"published":{"date-parts":[[2008,2,1]]}}}