This research aims to develop a supercomputing-based research tool based on validated and widely used docking approaches adapted for high-throughput screening of millions of compounds in a single day. Existing programs are adapted to use a Message Passing Interface (MPI) protocol to enable parallel computations of a target protein on thousands of processors simultaneously via massively parallel architectures. Virtual screening can now be run on over 65,000 processors in parallel on a supercomputer and essentially achieve in a day what used to take several weeks. These same tools can also be used to facilitate and expedite screening of prospective pharmaceuticals for toxicity and side effects. Importantly, this technological advance also allows the research community to simulate complex scenarios in cells containing multiple binding proteins, expanding isolated virtual in-vitro binding tests to multi-component virtual cell-based assays.