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MOTIVATION Human serum albumin (HSA), the most abundant plasma protein is well known for its extraordinary binding capacity for both endogenous and exogenous substances, including a wide range of drugs. Interaction with the two principal binding sites of HSA in subdomain IIA (site 1) and in subdomain IIIA (site 2) controls the free, active concentration of… (More)
Molecular docking is an important problem of bioinformatics aiming at the prediction of binding poses of molecules. Auto Dock is a popular, open-source docking software applying a computationally expensive but parallelizable algorithm. This paper introduces an FPGA-based and a GPU-based implementation of Auto Dock and shows how the original algorithm can be… (More)