Grid computing can integrate huge services and resources across distributed, heterogeneous, dynamic virtual organizations, and provide tremendous computing power in parallel. Workflow technology enables the user to compose complex Grid applications on distributed heterogeneous and unreliable hardware resources without taking care of lower level details. The drug discovery process almost comprises a number of sub processes, in which various software to be invoked, complex computing and huge amounts of data analyze are involved. Scientific workflow is the process of combining data and processes into a configurable, structured set of steps that implement semi-automated. Distributed processing and parallel computing capacity can improve the Computational efficiency. Therefore, the problems in drug discovery can be solved using the workflow technology. This paper discusses the problem on drug discovery process and presents how to utilize workflow in our eSOC System to resolve the three most important issues in drug discovery.