Graphics processing unit accelerated coarse-grained protein-protein docking

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.

Grantor dc:publisher.institution

Department of Computer Science

Year dc:date.issued

2011

Author dc:creator

• Tunbridge, Ian William

Advisors dc:contributor.advisor

• Kuttel, Michelle Mary
• Gain, JE
• Best, RB

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/11427/11670

OAI identifier oai:identifier

oai:open.uct.ac.za:11427/11670