Fast Docking on Graphics Processing Units via Ray-Casting
dc.contributor.author | Khar, Karen R. | |
dc.contributor.author | Goldschmidt, Lukasz | |
dc.contributor.author | Karanicolas, John | |
dc.date.accessioned | 2014-03-19T15:58:56Z | |
dc.date.available | 2014-03-19T15:58:56Z | |
dc.date.issued | 2013-08-16 | |
dc.identifier.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 | |
dc.identifier.uri | http://hdl.handle.net/1808/13254 | |
dc.description.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. | |
dc.description.sponsorship | This work was supported by grants from the National Institute of General Medical Sciences (1R01GM099959, 5R01GM095847), the National Institute on Aging (2R01AG029430 and 5P50AG016570), and the National Institute of Allergy and Infectious Diseases (5T32AI070089). | |
dc.publisher | Public Library of Science | |
dc.rights | ©2013 Khar et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. | |
dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | |
dc.subject | Biochemical simulation | |
dc.subject | Biophysical simulation | |
dc.subject | Complement inhibitors | |
dc.subject | Genetic algorithms | |
dc.subject | Library screening | |
dc.subject | Monte Carlo method | |
dc.subject | Optimization | |
dc.subject | Topography | |
dc.title | Fast Docking on Graphics Processing Units via Ray-Casting | |
dc.type | Article | |
kusw.kuauthor | Kahr, Karen R. | |
kusw.kuauthor | Karanicolas, John | |
kusw.kudepartment | Molecular Biosciences | |
kusw.oastatus | fullparticipation | |
dc.identifier.doi | 10.1371/journal.pone.0070661 | |
kusw.oaversion | Scholarly/refereed, publisher version | |
kusw.oapolicy | This item meets KU Open Access policy criteria. | |
dc.rights.accessrights | openAccess |
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Except where otherwise noted, this item's license is described as: ©2013 Khar et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.