MetalPredator: a web server to predict iron-sulfur cluster binding proteomes

MOTIVATION The prediction of the iron-sulfur proteome is highly desirable for biomedical and biological research but a freely available tool to predict iron-sulfur proteins has not been developed yet. RESULTS We developed a web server to predict iron-sulfur proteins from protein sequence(s). This tool, called MetalPredator, is able to process complete proteomes rapidly with high recall and precision. AVAILABILITY AND IMPLEMENTATION The web server is freely available at: http://metalweb.cerm.unifi.it/tools/metalpredator/ CONTACT andreini@cerm.unifi.it SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

[1]  R. Lill,et al.  Biogenesis of cytosolic and nuclear iron-sulfur proteins and their role in genome stability. , 2015, Biochimica et biophysica acta.

[2]  A. Rosato,et al.  Exploiting Bacterial Operons To Illuminate Human Iron-Sulfur Proteins. , 2016, Journal of proteome research.

[3]  Sean R. Eddy,et al.  Profile hidden Markov models , 1998, Bioinform..

[4]  Gabriele Cavallaro,et al.  MetalPDB: a database of metal sites in biological macromolecular structures , 2012, Nucleic Acids Res..

[5]  Lianyi Han,et al.  Prediction of the functional class of metal-binding proteins from sequence derived physicochemical properties by support vector machine approach , 2006, BMC Bioinformatics.

[6]  Antonio Rosato,et al.  A hint to search for metalloproteins in gene banks , 2004, Bioinform..

[7]  M. Fontecave,et al.  An integrative computational model for large-scale identification of metalloproteins in microbial genomes: a focus on iron-sulfur cluster proteins. , 2014, Metallomics : integrated biometal science.

[8]  Paolo Frasconi,et al.  MetalDetector v2.0: predicting the geometry of metal binding sites from protein sequence , 2011, Nucleic Acids Res..

[9]  Janet M. Thornton,et al.  Metal ions in biological catalysis: from enzyme databases to general principles , 2008, JBIC Journal of Biological Inorganic Chemistry.

[10]  V. Gladyshev,et al.  Comparative genomics analysis of the metallomes. , 2013, Metal ions in life sciences.

[11]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[12]  Gabriele Cavallaro,et al.  A Simple Protocol for the Comparative Analysis of the Structure and Occurrence of Biochemical Pathways Across Superkingdoms , 2011, J. Chem. Inf. Model..