Graphics processing unit accelerated coarse-grained protein-protein docking

Doctoral Thesis

2011

Permanent link to this Item
http://hdl.handle.net/11427/11670
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thesis_sci_2011_tunbridge_i.pdf (20.68 MB)
Authors
Tunbridge, Ian William
Supervisors
Kuttel, Michelle Mary
Gain, JE
Best, RB
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Publisher

University of Cape Town

Department
Department of Computer Science
Faculty
Faculty of Science
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Abstract
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.
Description

Includes abstract.


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

Reference:

Tunbridge, I. 2011. Graphics processing unit accelerated coarse-grained protein-protein docking. University of Cape Town.

Collections
PhD / Doctoral