Browsing by Author "Best, RB"
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- ItemOpen AccessGraphics processing unit accelerated coarse-grained protein-protein docking(2011) Tunbridge, Ian William; Kuttel, Michelle Mary; Gain, JE; Best, RBIn this work, we describe a Graphics processing unit (GPU) implementation of the Kim-Hummer coarse-grained model for protein docking simulations, using a Replica Exchange Monte-Carlo (REMC) method. Our highly parallel implementation vastly increases the size- and time scales accessible to molecular simulation. We describe in detail the complex process of migrating the algorithm to a GPU as well as the effect of various GPU approaches and optimisations on algorithm speed-up.