Molecular docking simulations have high potential to contribute to a wide area of molecular and biomedical research in various disciplines including molecular biology, drug design, environmental studies and psychology. Conducting large-scale molecular docking experiments requires a vast amount of computing resources. Several types of distributed computing infrastructures have been investigated and utilized recently to conduct such simulations, including service and desktop grid systems or local clusters. This paper investigates and analyses how Windows Azure-based cloud resources can be applied for this purpose. A virtual screening experiment framework has been implemented on a Windows Azure-based cloud using the generic worker concept. Virtual machines can be instantiated in the cloud on demand scaling up the simulations based on the volume of molecules to be docked and the available financial resources. Bioscientists are able to execute the simulations and visualise the results from a high-level user interface. The paper describes the experiences when implementing the molecular docking application on this novel platform and provides the first benchmarking experiments to evaluate the suitability of the infrastructure for computation intensive simulations. Copyright © 2013 John Wiley & Sons, Ltd.