DOCK Accessories - Revision history

Khtang at 22:43, 10 January 2019

2019-01-10T22:43:35Z

← Older revision		Revision as of 22:43, 10 January 2019
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	programs, the program DOCK matches spheres		programs, the program DOCK matches spheres
	(generated by [[sphgen]]) with ligand atoms and uses		(generated by [[sphgen]]) with ligand atoms and uses
	scoring grids (from [[grid)]] to		scoring grids (from [[grid]] to
	evaluate ligand orientations <ref name='kuntz1982' /><ref name='bks1992' />. Program DOCK also minimizes		evaluate ligand orientations <ref name='kuntz1982' /><ref name='bks1992' />. Program DOCK also minimizes
	energy based scores.<ref>[http://onlinelibrary.wiley.com/doi/abs/10.1002/prot.340170305 Meng EC, Gschwend DA, Blaney JM, Kuntz ID. Orientational sampling and rigid‐body minimization in molecular docking. Protein 17, 266-278(1993)]</ref>		energy based scores.<ref>[http://onlinelibrary.wiley.com/doi/abs/10.1002/prot.340170305 Meng EC, Gschwend DA, Blaney JM, Kuntz ID. Orientational sampling and rigid‐body minimization in molecular docking. Protein 17, 266-278(1993)]</ref>

Khtang: /* Main programs in DOCK suite */

2019-01-10T22:42:14Z

Main programs in DOCK suite

← Older revision		Revision as of 22:42, 10 January 2019
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	identifies the active site, and other sites of interest, and generates		identifies the active site, and other sites of interest, and generates
	the sphere centers that fill the site. It has been described in the		the sphere centers that fill the site. It has been described in the
	original paper ([[Kuntz ~~et al~~. J. Mol. Biol. 1982]]). The program [[grid]]		original paper <ref name='kuntz1982'>[http://www.sciencedirect.com/science/article/pii/002228368290153X?via%3Dihub Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE. A geometric approach to macromolecule-ligand interactions. J. Mol. Biol. 161, 269-288 (1982)]</ref>. The program [[grid]]
	generates the scoring grids <ref name='bks1992' >[http://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.540130311 Shoichet BK, Bodian DL, Kuntz ID. Molecular docking using shape descriptors. Journal of Computational Chemistry 13, 380-397 (1992).]</ref><ref>[http://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.540130412 Meng EC, Shoichet BK, Kuntz ID. Automated docking with grid-based energy evaluation. Journal of Computational Chemistry 13, 505-524 (1992).]</ref>. Within the DOCK suite of		generates the scoring grids <ref name='bks1992' >[http://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.540130311 Shoichet BK, Bodian DL, Kuntz ID. Molecular docking using shape descriptors. Journal of Computational Chemistry 13, 380-397 (1992).]</ref><ref>[http://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.540130412 Meng EC, Shoichet BK, Kuntz ID. Automated docking with grid-based energy evaluation. Journal of Computational Chemistry 13, 505-524 (1992).]</ref>. Within the DOCK suite of
	programs, the program DOCK matches spheres		programs, the program DOCK matches spheres
	(generated by [[sphgen]]) with ligand atoms and uses		(generated by [[sphgen]]) with ligand atoms and uses
	scoring grids (from [[grid)]] to		scoring grids (from [[grid)]] to
	evaluate ligand orientations <ref~~>[http:~~//www.sciencedirect.com/science/article/pii/002228368290153X?via%3Dihub Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE. A geometric approach to macromolecule-ligand interactions. J. Mol. Biol. 161, 269-288 (1982)]</ref><ref name='bks1992' />. Program DOCK also minimizes		evaluate ligand orientations <ref name='kuntz1982' /><ref name='bks1992' />. Program DOCK also minimizes
	energy based scores.<ref>[http://onlinelibrary.wiley.com/doi/abs/10.1002/prot.340170305 Meng EC, Gschwend DA, Blaney JM, Kuntz ID. Orientational sampling and rigid‐body minimization in molecular docking. Protein 17, 266-278(1993)]</ref>		energy based scores.<ref>[http://onlinelibrary.wiley.com/doi/abs/10.1002/prot.340170305 Meng EC, Gschwend DA, Blaney JM, Kuntz ID. Orientational sampling and rigid‐body minimization in molecular docking. Protein 17, 266-278(1993)]</ref>

	=References=		=References=
	<references />		<references />

Khtang: /* Main programs in DOCK suite */

2019-01-10T22:40:29Z

Main programs in DOCK suite

← Older revision		Revision as of 22:40, 10 January 2019
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	scoring grids (from [[grid)]] to		scoring grids (from [[grid)]] to
	evaluate ligand orientations <ref>[http://www.sciencedirect.com/science/article/pii/002228368290153X?via%3Dihub Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE. A geometric approach to macromolecule-ligand interactions. J. Mol. Biol. 161, 269-288 (1982)]</ref><ref name='bks1992' />. Program DOCK also minimizes		evaluate ligand orientations <ref>[http://www.sciencedirect.com/science/article/pii/002228368290153X?via%3Dihub Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE. A geometric approach to macromolecule-ligand interactions. J. Mol. Biol. 161, 269-288 (1982)]</ref><ref name='bks1992' />. Program DOCK also minimizes
	energy based scores.<ref>[~~https~~://onlinelibrary.wiley.com/doi/abs/10.1002/prot.340170305 Meng EC, Gschwend DA, Blaney JM, Kuntz ID. Orientational sampling and rigid‐body minimization in molecular docking. Protein 17, 266-278(1993)]</ref>		energy based scores.<ref>[http://onlinelibrary.wiley.com/doi/abs/10.1002/prot.340170305 Meng EC, Gschwend DA, Blaney JM, Kuntz ID. Orientational sampling and rigid‐body minimization in molecular docking. Protein 17, 266-278(1993)]</ref>

	=References=		=References=
	<references />		<references />

Khtang at 22:39, 10 January 2019

2019-01-10T22:39:25Z

← Older revision		Revision as of 22:39, 10 January 2019
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	the sphere centers that fill the site. It has been described in the		the sphere centers that fill the site. It has been described in the
	original paper ([[Kuntz et al. J. Mol. Biol. 1982]]). The program [[grid]]		original paper ([[Kuntz et al. J. Mol. Biol. 1982]]). The program [[grid]]
	generates the scoring grids		generates the scoring grids <ref name='bks1992' >[http://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.540130311 Shoichet BK, Bodian DL, Kuntz ID. Molecular docking using shape descriptors. Journal of Computational Chemistry 13, 380-397 (1992).]</ref><ref>[http://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.540130412 Meng EC, Shoichet BK, Kuntz ID. Automated docking with grid-based energy evaluation. Journal of Computational Chemistry 13, 505-524 (1992).]</ref>. Within the DOCK suite of
	([~~[Shoichet et al~~. J. ~~Comp~~. ~~Chem~~. 1992]~~] and~~
	[~~[Meng et al~~. J. ~~Comp~~. ~~Chem~~. 1992]]). Within the DOCK suite of
	programs, the program DOCK matches spheres		programs, the program DOCK matches spheres
	(generated by [[sphgen]]) with ligand atoms and uses		(generated by [[sphgen]]) with ligand atoms and uses
	scoring grids (from [[grid)]] to		scoring grids (from [[grid)]] to
	evaluate ligand orientations ([[Kuntz ~~et al~~. J. Mol. Biol. 1982]~~] and~~		evaluate ligand orientations <ref>[http://www.sciencedirect.com/science/article/pii/002228368290153X?via%3Dihub Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE. A geometric approach to macromolecule-ligand interactions. J. Mol. Biol. 161, 269-288 (1982)]</ref><ref name='bks1992' />. Program DOCK also minimizes
	~~[[Shoichet et al. J. Comp. Chem. 1992]])~~. Program DOCK also minimizes		energy based scores.<ref>[https://onlinelibrary.wiley.com/doi/abs/10.1002/prot.340170305 Meng EC, Gschwend DA, Blaney JM, Kuntz ID. Orientational sampling and rigid‐body minimization in molecular docking. Protein 17, 266-278(1993)]</ref>
	energy based scores ([[Meng ~~et al~~. ~~Proteins~~. 1993]~~]).~~
			=References=
			<references />

Sudipto: Created page with " The relationship between the main programs in the dock suite is depicted in Figure 1. These routines will be described below. < insert dock6_manual_files/dock_workflow.JPG >..."

2016-03-23T22:49:39Z

Created page with " The relationship between the main programs in the dock suite is depicted in Figure 1. These routines will be described below. < insert dock6_manual_files/dock_workflow.JPG >..."

New page

The relationship between the main
programs in the dock suite is depicted in Figure 1. These routines will
be described below.

< insert dock6_manual_files/dock_workflow.JPG >

= Main programs in DOCK suite =

The program [[sphgen]]
identifies the active site, and other sites of interest, and generates
the sphere centers that fill the site. It has been described in the
original paper ([[Kuntz et al. J. Mol. Biol. 1982]]). The program [[grid]]
generates the scoring grids
([[Shoichet et al. J. Comp. Chem. 1992]] and
[[Meng et al. J. Comp. Chem. 1992]]). Within the DOCK suite of
programs, the program DOCK matches spheres
(generated by [[sphgen]]) with ligand atoms and uses
scoring grids (from [[grid)]] to
evaluate ligand orientations ([[Kuntz et al. J. Mol. Biol. 1982]] and
[[Shoichet et al. J. Comp. Chem. 1992]]). Program DOCK also minimizes
energy based scores ([[Meng et al. Proteins. 1993]]).