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Fig. 1. The AMPA profile of eosinophile cationicprotein identifies the N-terminal (1-45) regionas antimicrobial. For experimental corroborationand further details, see ref. [2].The results of the AMPA screen werecompared with available data. Most ofthe proteins with known antimicrobialactivity in the training set werecorrectly identified and their antimicrobialdomains, wheneversufficient information on them wasavailable, accurately predicted. Inaddition, several de novo AMPAidentifiedsequences in proteins withhitherto unknown or poorly definedantimicrobial determinants wereexperimentally validated by means ofsynthetic versions of the AMPAdefinedregions. A case in point iseosinophile cationic protein, forwhich a strong antimicrobial motifwas identified in the N-terminalregion [2,3] (Figure 1).Taken together, the results ofapplying the AMPA algorithm to thetraining set were judged to be quitesatisfactory: high sensitivity (90%)and specificity (80%), with 85%average accuracy. To probe further itsreliability, AMPA was also applied toa positive testing set of 20 antimicrobial proteins, of which 90% were accurately predicted.A negative testing set was also screened, and 81% of the proteins were again correctlyidentified as non-antimicrobial. These results are in good agreement with those observedfor the training data set. In conclusion, AMPA is a useful, straightforward tool for detectingregions conferring antimicrobial properties to proteins. AMPA-selected regions may thusbecome starting points for the development of new AMP-derived drugs.AcknowledgmentsMT is the recipient of a postdoctoral grant from Alianza Cuatro Universidades (Spain). This work wassupported by grants BIO2008-04487-CO3-02 from the Spanish Ministry of Science and Innovation,SGR2005-00494 and SGR2009-00494 from Generalitat de Catalunya, and HEALTH-F3-2008-223414(Leishdrug) from the European Union.References1. Hilpert, K., Volkmer-Engert, R., Walter, T., Hancock, R.E. Nat. Biotech. 23, 1008-1012 (2005).2. Torrent, M., de la Torre, B.G., Nogués, M.V., Andreu, D., Boix, E. Biochem. J. 421, 425-434(2009).3. Torrent, M., Nogués, M.V., Boix, E. BMC Bioinf. 10, 373-382 (2009).419