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Bioinformatics Advance Access published online on July 16, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn371
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

MetalDetector: a web server for predicting metal binding sites and disulfide bridges in proteins from sequence

Marco Lippi 1, Andrea Passerini 1, Marco Punta 2,3,4, Burkhard Rost 2,3,4 and Paolo Frasconi 1,*

1Machine Learning and Neural Networks Group, Dipartimento di Sistemi e Informatica, Università degli Studi di Firenze, Via di Santa Marta 3, 50139 Firenze, Italy.
2Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, USA.
3Columbia University Center for Computational Biology and Bioinformatics (C2B2), 1130 St. Nicholas Ave., New York, NY 10032, USA.
4Northeast Structural Genomics Consortium (NESG), Columbia University, 1130 St. Nicholas Ave. Rm. 802, New York, NY 10032, USA

*To whom correspondence should be addressed. Prof. Paolo Frasconi, E-mail: p-f{at}dsi.unifi.it


  Abstract

Summary: The web server MetalDetector classifies histidine residues in proteins into one of two states (free, metal bound) and cysteines into one of three states (free, metal bound, disulfide bridged). A decision tree integrates predictions from two previously developed methods (DISULFIND, Metal Ligand Predictor). Cross-validated performance assessment indicates that our server predicts disulfide bonding state at 88.6% precision and 85.1% recall, while it identifies cysteines and histidines in transition metal binding sites at 79.9% precision and 76.8% recall and at 60.8% precision and 40.7% recall respectively.

Availability: Freely available at http://metaldetector.dsi.unifi.it.

Contact: metaldetector{at}dsi.unifi.it.

Supplementary Information: Details and data can be found at http://metaldetector.dsi.unifi.it/help.php

Associate Editor: Prof. John Quackenbush

Received on April 17, 2008; revised on June 27, 2008; accepted on July 14, 2008

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