DOI: 10.1093/bioinformatics/btn371. MetalDetector: a web server for predicting metal-binding sites and disulfide bridges in proteins from sequence

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

10.1093/bioinformatics/btn371

Crossref journal-article

Oxford University Press (OUP)

Bioinformatics (286)

Abstract

Abstract Summary: The web server MetalDetector classifies histidine residues in proteins into one of two states (free or metal bound) and cysteines into one of three states (free, metal bound or disulfide bridged). A decision tree integrates predictions from two previously developed methods (DISULFIND and 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@dsi.unifi.it Supplementary Information: Details and data can be found at http://metaldetector.dsi.unifi.it/help.php

Bibliography

Lippi, M., Passerini, A., Punta, M., Rost, B., & Frasconi, P. (2008). MetalDetector: a web server for predicting metal-binding sites and disulfide bridges in proteins from sequence. Bioinformatics, 24(18), 2094â2095.

Authors 5

Marco Lippi (first)
Andrea Passerini (additional)
Marco Punta (additional)
Burkhard Rost (additional)
Paolo Frasconi (additional)

References 7 Referenced 45

10.1093/nar/gkl266 / Nucleic Acids Res. / Disulfind: a disulfide bonding state and cysteine connectivity prediction server by Ceroni (2006)
10.1111/j.1742-4658.2007.05918.x / FEBS J. / The modulation of metal bio-availability as a therapeutic strategy for the treatment of alzheimer's disease by Crouch (2007)
10.1093/nar/gkl862 / Nucleic Acids Res. / Role of metal ions in catalysis by hiv integrase analyzed using a quantitative pcr disintegration assay by Diamond (2006)
10.1016/j.cbpc.2007.07.010 / Comp. Biochem. Physiol. C Toxicol. Pharmacol. / Zinc, antioxidant systems and metallothionein in metal mediated-apoptosis: biochemical and cytochemical aspects by Formigari (2007)
10.1089/rej.2006.9.351 / Rejuvenation Res. / Zinc homeostasis in aging: two elusive faces of the same ‘metal’ by Mocchegiani (2006)
10.1002/prot.21135 / Proteins / Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks by Passerini (2006)
10.1080/15287390600975004 / J. Toxicol. Environ. Health B Crit. Rev. / State-of-the-science review: Does manganese exposure during welding pose a neurological risk? by Santamaria (2007)

Dates

Type	When
Created	17 years, 1 month ago (July 17, 2008, 8:25 p.m.)
Deposited	2 years, 7 months ago (Feb. 2, 2023, 8:47 a.m.)
Indexed	4 minutes ago (Sept. 7, 2025, 9:04 a.m.)
Issued	17 years, 1 month ago (July 16, 2008)
Published	17 years, 1 month ago (July 16, 2008)
Published Online	17 years, 1 month ago (July 16, 2008)
Published Print	16 years, 11 months ago (Sept. 15, 2008)

Funders 0

None

BibTeX

@article{Lippi_2008, title={MetalDetector: a web server for predicting metal-binding sites and disulfide bridges in proteins from sequence}, volume={24}, ISSN={1367-4803}, url={http://dx.doi.org/10.1093/bioinformatics/btn371}, DOI={10.1093/bioinformatics/btn371}, number={18}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Lippi, Marco and Passerini, Andrea and Punta, Marco and Rost, Burkhard and Frasconi, Paolo}, year={2008}, month=jul, pages={2094–2095} }

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