PBSA Score - Revision history

Frodo at 04:01, 14 February 2014

2014-02-14T04:01:45Z

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	*** pbsa_vdw_grid_prefix [grid] (string):		*** pbsa_vdw_grid_prefix [grid] (string):
	**** The prefix to the grid files containing the VDW values		**** The prefix to the grid files containing the VDW values

			[[Category:Theory]]
			[[Category:Docking]]

Therese: 2 revisions

2012-10-08T20:31:13Z

2 revisions

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Rgc: hopefully formatting this page correctly

2009-11-17T20:11:41Z

hopefully formatting this page correctly

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			The PB/SA scoring function is an implementation of the ZAP tool kit from OpenEye. In order to access the PB/SA function, you must have the ZAP tool kit installed and a valid ZAP license. For more information on obtaining the tool kit, licensing, and other OpenEye products, go to the OpenEye web page at www.eyesopen.com
			15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)~~ From the OpenEye Documentation:

	~~The PB/SA scoring function is an implementation of the ZAP tool kit from OpenEye~~. ~~In order to access the PB/SA function~~, ~~you must have the ZAP tool kit installed and a valid ZAP license~~. ~~For more information on obtaining the tool kit, licensing,~~ and ~~other OpenEye products~~, ~~go to the OpenEye web page at www~~.~~eyesopen~~.~~com~~		"A Smooth Permittivity Function for Poisson-Boltzmann Solvation Methods", J. Andrew Grant, Barry T. Pickup and Anthony Nicholls, J. Comp. Chem, Vol 22, No.6, pgs 608-640, April 2001.
	~~15:54~~, ~~19 September 2006 (PDT)15:54~~, ~~19 September 2006 (PDT)15:54~~, ~~19 September 2006 (PDT)15:54~~, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)~~ From the OpenEye Documentation:

	~~"A Smooth Permittivity Function for~~ Poisson-Boltzmann ~~Solvation Methods"~~, J. ~~Andrew Grant~~, ~~Barry T~~. ~~Pickup~~ and ~~Anthony Nicholls~~, ~~J. Comp. Chem~~, ~~Vol 22~~, No.6, ~~pgs 608-640~~, ~~April 2001~~.		ZAP is, at its heart, a Poisson-Boltzmann (PB) solver. The Poisson equation describes how electrostatic fields change in a medium of varying dielectric, such as an organic molecule in water. The Boltzmann bit adds in the effect of mobile charge, e.g. salt. PB is an effective way to simulate the effects of water in biological systems. It relies on a charge description of a molecule, the designation of low (molecular) and high (solvent) dielectric regions and a description of an ion-accessible volume and produces a grid of electrostatic potentials. From this, transfer energies between different solvents, binding energies, pka shifts, pI's, solvent forces, electrostatic descriptors, solvent dipole moments, surface potentials and dielectric focusing can all be calculated. As electrostatics is one of the two principal components of molecular interaction (the other, of course, being shape), ZAP is OpenEye's attempt to get it right.

	ZAP is~~, at its heart, a Poisson-Boltzmann (PB) solver. The Poisson equation describes how electrostatic fields change~~ in a ~~medium~~ of ~~varying dielectric, such as an organic molecule~~ in ~~water~~. ~~The Boltzmann bit adds in~~ the ~~effect~~ of ~~mobile charge~~, e.~~g. salt. PB is an effective way~~ to ~~simulate~~ the ~~effects~~ of ~~water in biological systems. It relies on a charge description of a molecule,~~ the designation of low (molecular) and high (solvent) dielectric regions and a description of an ion-accessible volume and produces a grid of electrostatic potentials. From this, transfer energies between different solvents, binding energies, pka shifts, pI's, solvent forces, electrostatic descriptors, solvent dipole moments, ~~surface potentials and dielectric focusing can all be calculated. As electrostatics is one of~~ the ~~two principal components of molecular interaction (the other, of course, being shape), ZAP is OpenEye's attempt to get it right~~.		ZAP is written in ANSI C and follows a style of object-oriented programming popularized in the chemical information world by Daylight. It encapsulates structures and methods by the use of opaque pointers, or handles. These are integers converted to real pointers in the interior of the object system, hidden from the user.

	ZAP is written in ANSI C and follows a style of object-oriented programming popularized in the chemical information world by Daylight. It encapsulates structures and methods by the use of opaque pointers, or handles. These are integers converted to real pointers in the interior of the object system, hidden from the user.		ZAP is available to most academic and government institutions free of charge. It comes in the form of a linkable library and a set of prepackaged binaries compiled for SGI, Linux and Cygwin (NT). Commercial use requires a license, available at a very reasonable cost from the nice folks at OpenEye. 15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)~~
	ZAP is available to most academic and government institutions free of charge. It comes in the form of a linkable library and a set of prepackaged binaries compiled for SGI, Linux and Cygwin (NT). Commercial use requires a license, available at a very reasonable cost from the nice folks at OpenEye. 15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)~~

	NOTE: The following parameter definitions will use the format below:		NOTE: The following parameter definitions will use the format below:

	parameter_name [default] (value):		parameter_name [default] (value):
	#description		#description

	In some cases, parameters are only needed (questions will only be asked) if the parameter above is enforced. These parameters are indicated below by additional indentation.		In some cases, parameters are only needed (questions will only be asked) if the parameter above is enforced. These parameters are indicated below by additional indentation.

	PB/SA Score Parameters		PB/SA Score Parameters

	* pbsa_score_primary [yes] (yes, no):		* pbsa_score_primary [yes] (yes, no):
	# Flag to perform pbsa energy scoring as the primary scoring		** Flag to perform pbsa energy scoring as the primary scoring
	#function		**function
	* pbsa_score_secondary [yes] (yes, no):		* pbsa_score_secondary [yes] (yes, no):
	# Flag to perform pbsa energy scoring as the secondary		** Flag to perform pbsa energy scoring as the secondary
	#scoring function		**scoring function
	o pbsa_receptor_filename [receptor.mol2] (string):		*** pbsa_receptor_filename [receptor.mol2] (string):
	# Name of receptor file.		**** Name of receptor file.
	o pbsa_interior_dielectric [2.0] (float):		*** pbsa_interior_dielectric [2.0] (float):
	# Value for the dielectric inside the protein		**** Value for the dielectric inside the protein
	o pbsa_exterior_dielectric [78.5] (float):		*** pbsa_exterior_dielectric [78.5] (float):
	# Value for the dielectric of the solvent (outside the protein)		**** Value for the dielectric of the solvent (outside the protein)
	o pbsa_vdw_grid_prefix [grid] (string):		*** pbsa_vdw_grid_prefix [grid] (string):
	# The prefix to the grid files containing the VDW values		**** The prefix to the grid files containing the VDW values

JohnIrwin at 22:54, 19 September 2006

2006-09-19T22:54:54Z

New page

The PB/SA scoring function is an implementation of the ZAP tool kit from OpenEye. In order to access the PB/SA function, you must have the ZAP tool kit installed and a valid ZAP license. For more information on obtaining the tool kit, licensing, and other OpenEye products, go to the OpenEye web page at www.eyesopen.com
15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)~~ From the OpenEye Documentation:

"A Smooth Permittivity Function for Poisson-Boltzmann Solvation Methods", J. Andrew Grant, Barry T. Pickup and Anthony Nicholls, J. Comp. Chem, Vol 22, No.6, pgs 608-640, April 2001.

ZAP is, at its heart, a Poisson-Boltzmann (PB) solver. The Poisson equation describes how electrostatic fields change in a medium of varying dielectric, such as an organic molecule in water. The Boltzmann bit adds in the effect of mobile charge, e.g. salt. PB is an effective way to simulate the effects of water in biological systems. It relies on a charge description of a molecule, the designation of low (molecular) and high (solvent) dielectric regions and a description of an ion-accessible volume and produces a grid of electrostatic potentials. From this, transfer energies between different solvents, binding energies, pka shifts, pI's, solvent forces, electrostatic descriptors, solvent dipole moments, surface potentials and dielectric focusing can all be calculated. As electrostatics is one of the two principal components of molecular interaction (the other, of course, being shape), ZAP is OpenEye's attempt to get it right.

ZAP is written in ANSI C and follows a style of object-oriented programming popularized in the chemical information world by Daylight. It encapsulates structures and methods by the use of opaque pointers, or handles. These are integers converted to real pointers in the interior of the object system, hidden from the user.
ZAP is available to most academic and government institutions free of charge. It comes in the form of a linkable library and a set of prepackaged binaries compiled for SGI, Linux and Cygwin (NT). Commercial use requires a license, available at a very reasonable cost from the nice folks at OpenEye. 15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)15:54, 19 September 2006 (PDT)~~

NOTE: The following parameter definitions will use the format below:

parameter_name [default] (value):
#description

In some cases, parameters are only needed (questions will only be asked) if the parameter above is enforced. These parameters are indicated below by additional indentation.

PB/SA Score Parameters

* pbsa_score_primary [yes] (yes, no):
# Flag to perform pbsa energy scoring as the primary scoring
#function
* pbsa_score_secondary [yes] (yes, no):
# Flag to perform pbsa energy scoring as the secondary
#scoring function
o pbsa_receptor_filename [receptor.mol2] (string):
# Name of receptor file.
o pbsa_interior_dielectric [2.0] (float):
# Value for the dielectric inside the protein
o pbsa_exterior_dielectric [78.5] (float):
# Value for the dielectric of the solvent (outside the protein)
o pbsa_vdw_grid_prefix [grid] (string):
# The prefix to the grid files containing the VDW values