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...
| Main Author: | |
|---|---|
| Other Authors: | |
| Format: | Doctoral Thesis |
| Language: | English |
| Published: |
University of Cape Town
2015
|
| Online Access: | http://hdl.handle.net/11427/11670 |
| Summary: | 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. |
|---|