AMPA is a web application for assessing the antimicrobial domains of proteins, with a focus on the design on new antimicrobial drugs. The application provides fast discovery of antimicrobial patterns in proteins that can be used to develop new peptidebased drugs against pathogens. Results are shown in a user-friendly graphical interface and can be downloaded as raw data for later examination. © The Author 2011. Published by Oxford University Press. All rights reserved.