ePubs

The open archive for STFC research publications

Full Record Details

Persistent URL	http://purl.org/net/epubs/work/40886
Record Status	Checked
Record Id	40886
Title	Ab Initio potential grid based docking: From High Performance Computing to In Silico Screening
Contributors	MR de Jonge (MolMo Services BVBA), HM Vinkers (MolMo Services BVBA), JH van Lenthe (Utrecht U.), F Daeyaert (MolMo Services BVBA), IJ Bush (Science and Technology Facilities Council), HJJ van Dam (Science and Technology Facilities Council), P Sherwood (Science and Technology Facilities Council), MF Guest (Cardiff U.), A Siebes (American Institute of Physics) (Ed.), M Berthold (American Institute of Physics) (Ed.), R Glen (American Institute of Physics) (Ed.), A Feelders (American Institute of Physics) (Ed.)
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
Funding Information
Related Research Object(s):
Licence Information:
Language	English (EN)

Type	Details	URI(s)	Local file(s)	Year
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