Methodology article

A theoretical approach to spot active regions in antimicrobial proteins

Marc Torrent , Victòria M Nogués and Ester Boix

Dpt. Bioquímica i Biologia Molecular, Fac. Biociències, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain

author email corresponding author email

BMC Bioinformatics 2009, 10:373doi:10.1186/1471-2105-10-373

Published:	11 November 2009

Abstract

Background

Much effort goes into identifying new antimicrobial compounds able to evade the increasing resistance of microorganisms to antibiotics. One strategy relies on antimicrobial peptides, either derived from fragments released by proteolytic cleavage of proteins or designed from known antimicrobial protein regions.

Results

To identify these antimicrobial determinants, we developed a theoretical approach that predicts antimicrobial proteins from their amino acid sequence in addition to determining their antimicrobial regions. A bactericidal propensity index has been calculated for each amino acid, using the experimental data reported from a high-throughput screening assay as reference. Scanning profiles were performed for protein sequences and potentially active stretches were identified by the best selected threshold parameters. The method was corroborated against positive and negative datasets. This successful approach means that we can spot active sequences previously reported in the literature from experimental data for most of the antimicrobial proteins examined.

Conclusion

The method presented can correctly identify antimicrobial proteins with an accuracy of 85% and a sensitivity of 90%. The method can also predict their key active regions, making this a tool for the design of new antimicrobial drugs.