PepMapper has been implemented using C++ as a Web-based tool located at http://informatics.nenu.edu.cn/PepMapper. It is currently deployed on Linux using tomcat server 6.0 and has been tested using many popular Web browsers, such as IE7-9, Firefox, and Opera. Three options, MimoPro, Pep-3D-Search, and their combination, are available for the users to choose for the purpose of their applications. Note that the original Web tool of Pep-3D-Search was implemented using VB.NET. Pep-3D-Search in PepMapper is re-implemented using C++ and a modified ACO algorithm is adopted for more efficient searching (See Table S1 for details).