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Because of their functional and sequence diversity, it is desirable to explore additional methods for predicting metal-binding proteins irrespective of sequence similarity. This work explores support vector machines (SVM) as such a method. SVM prediction systems were developed by using 53,333 metal-binding and 147,347 non-metal-binding proteins, and evaluated by an independent set of 31,448 metal-binding and 79,051 non-metal-binding proteins. The computed prediction accuracy is 86.3%, 81.6%, 83.5%, 94.0%, 81.2%, 85.4%, 77.6%, 90.4%, 90.9%, 74.9% and 78.1% for calcium-binding, cobalt-binding, copper-binding, iron-binding, magnesium-binding, manganese-binding, nickel-binding, potassium-binding, sodium-binding, zinc-binding, and all metal-binding proteins respectively. The accuracy for the non-member proteins of each class is 88.2%, 99.9%, 98.1%, 91.4%, 87.9%, 94.5%, 99.2%, 99.9%, 99.9%, 98.0%, and 88.0% respectively. Comparable accuracies were obtained by using a different SVM kernel function. Our method predicts 67% of the 87 metal-binding proteins non-homologous to any protein in the Swissprot database and 85.3% of the 333 proteins of known metal-binding domains as metal-binding. These suggest the usefulness of SVM for facilitating the prediction of metal-binding proteins. Our software can be accessed at the SVMProt server <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/jing.cz3.nus.edu.sg\/cgi-bin\/svmprot.cgi\" ext-link-type=\"uri\">http:\/\/jing.cz3.nus.edu.sg\/cgi-bin\/svmprot.cgi<\/jats:ext-link>.<\/jats:p>","DOI":"10.1186\/1471-2105-7-s5-s13","type":"journal-article","created":{"date-parts":[[2006,12,19]],"date-time":"2006-12-19T07:16:56Z","timestamp":1166512616000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":52,"title":["Prediction of the functional class of metal-binding proteins from sequence derived physicochemical properties by support vector machine approach"],"prefix":"10.1186","volume":"7","author":[{"given":"HH","family":"Lin","sequence":"first","affiliation":[]},{"given":"LY","family":"Han","sequence":"additional","affiliation":[]},{"given":"HL","family":"Zhang","sequence":"additional","affiliation":[]},{"given":"CJ","family":"Zheng","sequence":"additional","affiliation":[]},{"given":"B","family":"Xie","sequence":"additional","affiliation":[]},{"given":"ZW","family":"Cao","sequence":"additional","affiliation":[]},{"given":"YZ","family":"Chen","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2006,12,18]]},"reference":[{"issue":"48","key":"1363_CR1","doi-asserted-by":"publisher","first-page":"47644","DOI":"10.1074\/jbc.M309338200","volume":"278","author":"H Wintz","year":"2003","unstructured":"Wintz H, Fox T, Wu YY, Feng V, Chen W, Chang HS, Zhu T, Vulpe C: Expression profiles of Arabidopsis thaliana in mineral deficiencies reveal novel transporters involved in metal homeostasis. 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