Graphics processing unit accelerated coarse-grained protein-protein docking

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...

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Bibliographic Details
Main Author:	Tunbridge, Ian William
Other Authors:	Kuttel, Michelle Mary
Format:	Doctoral Thesis
Language:	English
Published:	University of Cape Town 2015
Online Access:	http://hdl.handle.net/11427/11670

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spelling	ndltd-netd.ac.za-oai-union.ndltd.org-uct-oai-localhost-11427-116702020-07-22T05:07:39Z Graphics processing unit accelerated coarse-grained protein-protein docking Tunbridge, Ian William Kuttel, Michelle Mary Gain, JE Best, RB 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. 2015-01-06T19:04:46Z 2015-01-06T19:04:46Z 2011 Doctoral Thesis Doctoral PhD http://hdl.handle.net/11427/11670 eng application/pdf University of Cape Town Faculty of Science Department of Computer Science
collection	NDLTD
language	English
format	Doctoral Thesis
sources	NDLTD
description	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.
author2	Kuttel, Michelle Mary
author_facet	Kuttel, Michelle Mary Tunbridge, Ian William
author	Tunbridge, Ian William
spellingShingle	Tunbridge, Ian William Graphics processing unit accelerated coarse-grained protein-protein docking
author_sort	Tunbridge, Ian William
title	Graphics processing unit accelerated coarse-grained protein-protein docking
title_short	Graphics processing unit accelerated coarse-grained protein-protein docking
title_full	Graphics processing unit accelerated coarse-grained protein-protein docking
title_fullStr	Graphics processing unit accelerated coarse-grained protein-protein docking
title_full_unstemmed	Graphics processing unit accelerated coarse-grained protein-protein docking
title_sort	graphics processing unit accelerated coarse-grained protein-protein docking
publisher	University of Cape Town
publishDate	2015
url	http://hdl.handle.net/11427/11670
work_keys_str_mv	AT tunbridgeianwilliam graphicsprocessingunitacceleratedcoarsegrainedproteinproteindocking
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Graphics processing unit accelerated coarse-grained protein-protein docking

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