In the study of Biomedicines, molecular docking simulation is a common method for predicting potential interacting complexes of small molecules in protein binding sites. However, it is a time-consuming process to search exhaustively all correct conformations of a compound. This study demonstrates how massive molecular docking benefit from state-of-the-art Grid technology. Providing intensive computing power and effective data management, the production e-infrastructure (such as EGEE and EUAsiaGrid) enables opportunities for in-silico drug discovery on the neglected and emerging diseases, for instance, avian influenza and dengue fever. In this study, Grid Application Platform (GAP) and GAP-enabled Virtual Screening Service (GVSS) were developed with the docking engine of the Autodock 3.0.5. A JAVA-based graphical user interface and the GAP allow end-users to specify target and compound library, set up docking parameters, monitor docking jobs and computing resources, visualize and refine docking results, and finally download the final results. To provide a more user-friendly Grid service, GVSS was designed for conducting large-scale molecular docking more easily.

The first and second grid challenges preparing for avian flu drug discovery in mutations have demonstrated that the biomedical communities can be largely benefited from the EGEE infrastructure in terms of the speed and the reaction time of screening over a full spectrum of the compound libraries. Based on Grid Application Platform (GAP)