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A GPU-Based Approach to Accelerate Computational Protein-DNA Docking
May/June 2012 (vol. 14 no. 3)
pp. 20-29
Jiadong Wu, Georgia Institute of Technology
Chunlei Chen, Georgia Institute of Technology
Bo Hong, Georgia Institute of Technology

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.

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Index Terms:
Protein-DNA docking, Monte Carlo simulation, GPU, CUDA, scientific computing
Citation:
Jiadong Wu, Chunlei Chen, Bo Hong, "A GPU-Based Approach to Accelerate Computational Protein-DNA Docking," Computing in Science and Engineering, vol. 14, no. 3, pp. 20-29, May-June 2012, doi:10.1109/MCSE.2011.118
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