A molecular docking is the process of reducing an unmanageable number of compounds to a limited number of compounds for the target of interest by means of computational simulation. And it is one of a large-scale scientific application that requires large computing power and data storage capability. Previous applications or software for molecular docking were developed to be run on a supercomputer, a workstation, or a cluster-computer. However the molecular docking using a supercomputer has a problem that a supercomputer is very expensive and the molecular docking using a workstation or a cluster-computer requires a long execution time. Thus we propose Grid service-based molecular docking application. We designed a resource broker and a data broker for supporting efficient molecular docking service and developed various services for molecular docking. Our application can reduce a timeline and cost of drug or new material design.