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Fast Docking on Graphics Processing Units via Ray-Casting
Khar, Karen R. Goldschmidt, Lukasz Karanicolas, John
Khar, Karen R.
Goldschmidt, Lukasz
Karanicolas, John
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Abstract
Docking Approach using Ray Casting (DARC) is structure-based computational method for carrying out virtual screening by docking small-molecules into protein surface pockets. In a complementary study we find that DARC can be used to identify known inhibitors from large sets of decoy compounds, and can identify new compounds that are active in biochemical assays. Here, we describe our adaptation of DARC for use on Graphics Processing Units (GPUs), leading to a speedup of approximately 27-fold in typical-use cases over the corresponding calculations carried out using a CPU alone. This dramatic speedup of DARC will enable screening larger compound libraries, screening with more conformations of each compound, and including multiple receptor conformations when screening. We anticipate that all three of these enhanced approaches, which now become tractable, will lead to improved screening results.
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2013-08-16
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Public Library of Science
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Khar.pdf
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Biochemical simulation, Biophysical simulation, Complement inhibitors, Genetic algorithms, Library screening, Monte Carlo method, Optimization, Topography
Citation
Khar, K. R., Goldschmidt, L., & Karanicolas, J. (2013). Fast Docking on Graphics Processing Units via Ray-Casting. PLoS ONE, 8(8). http://dx.doi.org/10.1371/journal.pone.0070661