Zou-GBA Score - Revision history

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2012-10-08T20:33:21Z

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JohnIrwin at 21:19, 20 September 2007

2007-09-20T21:19:04Z

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	The Zou GB/SA scoring function is a fast algorithm, the pairwise free energy model, for ligand binding affinity calculations. Specifically, a pairwise descreening approximation (Hawkins, et al. Chem. Phys. Lett. 1995) is used in calculations of the electrostatic energy contribution. The algorithm also includes a procedure to account for the low dielectric region that might form between the ligand and the receptor during docking processes. It has been tested to obtain similar results compared with the grid-based free energy model but with much less computation efforts.		The Zou GB/SA scoring function is a fast algorithm, the pairwise free energy model, for ligand binding affinity calculations. Specifically, a pairwise descreening approximation (Hawkins, et al. Chem. Phys. Lett. 1995) is used in calculations of the electrostatic energy contribution. The algorithm also includes a procedure to account for the low dielectric region that might form between the ligand and the receptor during docking processes. It has been tested to obtain similar results compared with the grid-based free energy model but with much less computation efforts.
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	o gbsa_zou_solvent_dielectric [78.300003] (float):		o gbsa_zou_solvent_dielectric [78.300003] (float):
	# The value for the solvent dielectric		# The value for the solvent dielectric



			[[Category:DOCK:Scoring problem]]

JohnIrwin at 22:54, 19 September 2006

2006-09-19T22:54:09Z

New page

The Zou GB/SA scoring function is a fast algorithm, the pairwise free energy model, for ligand binding affinity calculations. Specifically, a pairwise descreening approximation (Hawkins, et al. Chem. Phys. Lett. 1995) is used in calculations of the electrostatic energy contribution. The algorithm also includes a procedure to account for the low dielectric region that might form between the ligand and the receptor during docking processes. It has been tested to obtain similar results compared with the grid-based free energy model but with much less computation efforts.

For more information on the scoring function and specifics of the implementation, see Liu, et al J. Phys. Chem. B. 2004.

Zou GB/SA Score Parameters

* gbsa_zou_score_primary [no] (yes, no):
#Flag to perform Zou GB/SA scoring as the primary scoring
#function
* gbsa_zou_score_secondary [no] (yes, no):
#Flag to perform Zou GB/SA scoring as the secondary scoring
#function
o gbsa_zou_gb_grid_prefix [gb_grid] (string):
# The path to the pairwise GB grids
o gbsa_zou_sa_grid_prefix [sa_grid] (string):
#The path to the SA grids
o gbsa_zou_vdw_grid_prefix [grid] (string):
#The path to the nrg grids, used for the vdw portion of the GB/SA calculation
o gbsa_zou_screen_file [screen.in] (string):
# GB parameter file for electrostatic screening. Its located in the parameters dir by default
o gbsa_zou_solvent_dielectric [78.300003] (float):
# The value for the solvent dielectric