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Issue No. 03 - May/June (2012 vol. 14)
ISSN: 1521-9615
pp: 20-29
Jiadong Wu , Georgia Institute of Technology
Chunlei Chen , Georgia Institute of Technology
Bo Hong , Georgia Institute of Technology
<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>
Protein-DNA docking, Monte Carlo simulation, GPU, CUDA, scientific computing

C. Chen, B. Hong and J. Wu, "A GPU-Based Approach to Accelerate Computational Protein-DNA Docking," in Computing in Science & Engineering, vol. 14, no. , pp. 20-29, 2011.
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