Molecular docking and virtual screening experiments require large computational and data resources and high-level user interfaces in the form of science gateways. While science gateways supporting such experiments are relatively common, there is a clearly identified need to design and implement more complex environments for further analysis of docking results. This paper describes a generic framework and a related methodology that supports the efficient development of such environments. The framework is modular enabling the reuse of already existing components. The methodology is agile and encourages the input and participation of end-users. A prototype implementation, based on the framework and methodology, of a science-gateway-based molecular docking environment for recommending a ligand-protein pair for next docking experiment is also presented and evaluated
