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Issue No.03 - May/June (2012 vol.14)
pp: 20-29
Chunlei Chen , Georgia Institute of Technology
Jiadong Wu , Georgia Institute of Technology
ABSTRACT
<p>This article describes a GPU-based high-performance computing method to tackle the protein-DNA docking problem. GPU-specific algorithmic techniques are developed to accelerate a docking algorithm that integrates Monte Carlo simulation and simulated annealing. Experiments show that such improved computation speed accelerates the conformational space sampling of the algorithm and increases the chance of finding near-native protein-DNA structures.</p>
INDEX TERMS
Protein-DNA docking, Monte Carlo simulation, GPU, CUDA, scientific computing
CITATION
Chunlei Chen, Jiadong Wu, "A GPU-Based Approach to Accelerate Computational Protein-DNA Docking", Computing in Science & Engineering, vol.14, no. 3, pp. 20-29, May/June 2012, doi:10.1109/MCSE.2011.118
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