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thesis
oaioai:open.uct.ac.za:11427/11670

Graphics processing unit accelerated coarse-grained protein-protein docking

Authors
Publication date
1 January 2011
Publisher
'University of Cape Town'

Abstract

Includes abstract.Includes bibliographical references (leaves [187]-202).In 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

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This paper was published in Cape Town University OpenUCT.

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