High-throughput virtual molecular docking
Sally R. Ellingson, Jerome Y. Baudry · 2011
Virtual molecular docking is a computational method used in computer-aided drug discovery that calculates the binding affinity of a small molecule drug candidate to a target protein and greatly reduces the time and cost of suggesting new potential pharmaceuticals. This high-throughput screening is a task parallel process and therefore well suited for distributed computing. In this study, we use the open source Hadoop framework implementing the MapReduce paradigm for distributed computing on a cloud platform and the widely used molecular docking program AutoDock. Our high-throughput virtual docking implementation, AutoDockCloud, showed a speed-up of 450 on Kandinsky, a cloud computer located at Oak Ridge National Laboratory.