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Issue No.06 - Nov.-Dec. (2013 vol.15)
pp: 64-72
Denis Navarro , Univ. of Zaragoza, Zaragoza, Spain
Oscar Lucia , Univ. of Zaragoza, Zaragoza, Spain
Jose M. Gil-Narvion , Univ. of Zaragoza, Zaragoza, Spain
Oscar Jimenez , Univ. of Zaragoza, Zaragoza, Spain
ABSTRACT
Virtual screening is a key process used to identify the most suitable molecule combinations when developing a new drug. Molecule docking is a commonly used method to analyze molecule structures and requires computing large databases to identify possible affinities between molecules. The special-purpose, field-programmable gate array (FPGA)-based Janus supercomputer accelerates the virtual screening process.
INDEX TERMS
Field programmable gate arrays, Acceleration, Computer architecture, Signal processing algorithms, Databases, Virtual environments, Three-dimensional displays,special-purpose hardware, Field programmable gate arrays, Acceleration, Computer architecture, Signal processing algorithms, Databases, Virtual environments, Three-dimensional displays, scientific computing, hardware description languages, algorithms implemented in hardware
CITATION
Denis Navarro, Oscar Lucia, Jose M. Gil-Narvion, Oscar Jimenez, "FPGA-Based Virtual Screening Acceleration of Rigid-Molecule Docking", Computing in Science & Engineering, vol.15, no. 6, pp. 64-72, Nov.-Dec. 2013, doi:10.1109/MCSE.2012.88
REFERENCES
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2. F. Belletti et al., “Ianus: An Adaptive FPGA Computer,” Computing in Science and Eng., vol. 8, no. 1, 2006, pp. 41-49.
3. F. Belletti et al., “Janus: An FPGA-Based System for High-Performance Scientific Computing,” Computing in Science and Eng., vol. 11, no. 1, 2009, pp. 48-58.
4. D. Qiwen and Z. Shuigeng, “Novel Nonlinear Knowledge-Based Mean Force Potentials Based on Machine Learning,” IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 8, no. 2, 2011, pp. 476-486.
5. T. Ching-Chih, H. Hsu-Chih, and L. Shui-Chun, “FPGA-Based Parallel DNA Algorithm for Optimal Configurations of an Omnidirectional Mobile Service Robot Performing Fire Extinguishment,” IEEE Trans. Industrial Electronics, vol. 58, no. 3, 2011, pp. 1016-1026.
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