Abstract: Systems and methods for integrating a computer-aided molecular discovery process across a plurality of computer-aided molecular discovery applications are described. In one embodiment, an integrated user interface provides the user with access to the capabilities from a broad array of commercial and custom application modules, such as calculation engines. In another embodiment of this invention a heterogeneous cluster provides the ability to divide the processing required for a molecular discovery process to increase efficiency and reduce the time required to perform molecular discovery.