A theoretical approach to spot active regions in antimicrobial proteins

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.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.Host defence anti-microbial proteins and peptides are important participants of the innate immune response in most multicellular organisms [1]. The innate immune system comprises the cells and mechanisms that defend the host from infection by other organisms in a non-specific manner. Unlike the adaptive immune system, the innate immune system does not confer a long-lasting or protective immunity to the host, but is thought to constitute an evolutionarily older defence strategy. It remains the dominant immune system in plants, fungi and insects, and plays a crucial role during the first steps of infection in multicellular organisms.One of the major achievements of medicine was the development of antibiotics, which can kill a broad spectrum of microorganisms. Unfortunately, the emergence of antibiotic resistance has become a clinical threat [2,3]. Cationic proteins and peptides that are involved in innate immunity represent an alternative strategy to conventional antibiotics [4]. A considerable va