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Persistent URL http://purl.org/net/epubs/work/40886
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Record Id 40886
Title Ab Initio potential grid based docking: From High Performance Computing to In Silico Screening
Abstract We present a new method for the generation of potential grids for protein-ligand docking. The potential of the docking target structure is obtained directly from the electron density derived through an ab initio computation. A large subregion was selected to allow the full ab initio treatment of a the Isocitrate Lyase enzyme. The electrostatic potential is tested by docking a small charged molecule (succinate) into the binding site. The ab initio grid yields a superior result by producing the best binding orientation and position, and by recognizing it as the best. In contrast the same docking procedure, but using a classical point-charge based potential, produces a number of additional incorrect binding poses, and does not recognize the correct pose as the best solution.
Organisation CCLRC , CSE , CSE-CCG , CSE-HEC
Keywords Chemistry , grid , Ab Initio Docking Algorithm , ABIDA , docking , electrostatic potential
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Language English (EN)
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Paper In Conference Proceedings AIP Conference Proceedings 940, pp 168-178. Is in proceedings of: The 3rd International Symposium on Computational Life Science (CompLife 2007), Utrecht, 4-5 Oct 2007. doi:10.1063/1.2793399 2007