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GPU-Accelerated Computation of Solvation Free Energy for Kinetostatic Protein Folding Simulation

[+] Author Affiliations
Morad Behandish, Pouya Tavousi, Horea T. Ilieş, Kazem Kazerounian

University of Connecticut, Storrs, CT

Paper No. DETC2013-12675, pp. V02AT02A009; 12 pages
doi:10.1115/DETC2013-12675
From:
  • ASME 2013 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference
  • Volume 2A: 33rd Computers and Information in Engineering Conference
  • Portland, Oregon, USA, August 4–7, 2013
  • Conference Sponsors: Design Engineering Division, Computers and Information in Engineering Division
  • ISBN: 978-0-7918-5585-0
  • Copyright © 2013 by ASME

abstract

A realistic computer simulation of protein folding requires a comprehensive account of interaction energetics, placing a substantial demand on processing power. This paper presents an improved computational framework for protein folding software package PROTOFOLD, that enables efficient computation of solvation free energy effects in addition to Coulombic and van der Waals interactions. Efficient data structures have been utilized to speed-up the sequential running times from O(n2) to O(n), n being the number of atoms. It turns out, however, that an accurate evaluation of molecular surface areas characterizing the solvation effects imposes a computational bottleneck to the entire simulation. Massive computational power offered by Graphics Processing Units (GPU) was exploited to develop a simple and efficient Single-Instruction Multiple-Thread (SIMT) algorithm for the latter step. The running times were monitored for different steps of the folding simulation for different molecular sizes. Significant performance improvements were observed, yielding promising results where numerous iterative runs are needed.

Copyright © 2013 by ASME

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