Ab initio protein structure prediction usingGPU computing

Dubey, Sandhya P and Kini, Gopalakrishna N and Kumar, Sathish M and Balaji, S (2016) Ab initio protein structure prediction usingGPU computing. Perspectives in Science, 8. pp. 645-647.

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Abstract

Graphics processing unit (GPU) accelerated computing has pioneered a new direc-tion of research for various combinatorial optimization problems. One such problem whichrequires huge computation is protein structure prediction (PSP). PSP is NP-complete problem.Computational prediction of protein native structure from its primary amino acid sequence istermed as ab initio PSP problem. Till date, wet lab experiments conducted on PSP indicate thatexisting methods take lots of experimentation time and expensive. As a consequence, only 1%of the sequence’s structures are known. This work presents a parallel programming approachwith GPU computing for PSP using 2D triangular hydrophobic-polar (HP) lattice model. Theimplementation of proposed approach is tested on the set of HP benchmark sequence of alength ranging from 25 to 100. The experimental result shows that the proposed approach hassignificantly improved the performance of prediction with immense drop in computation time.© 2016 Published by Elsevier GmbH. This is an open access article under the CC BY-NC-ND license

Item Type: Article
Uncontrolled Keywords: 2016KEYWORDSProtein structureprediction;Hydrophobic-polarmodel;NP-problem;Parallelprogramming;Graphics processingunit;EvolutionaryprogrammingSummary
Subjects: Engineering > MIT Manipal > Biotechnology
Engineering > MIT Manipal > Computer Science and Engineering
Engineering > MIT Manipal > Electronics and Communication
Depositing User: MIT Library
Date Deposited: 20 Oct 2016 13:29
Last Modified: 20 Oct 2016 13:29
URI: http://eprints.manipal.edu/id/eprint/147286

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