Dock - Revision history

Frodo: Redirected page to Category:DOCK

2014-02-15T17:33:39Z

← Older revision		Revision as of 17:33, 15 February 2014
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	~~see~~ [[Category:DOCK]]		#REDIRECT [[Category:DOCK]]

Frodo: Replaced content with "see Category:DOCK"

2014-02-14T16:31:53Z

Replaced content with "see Category:DOCK"

← Older revision		Revision as of 16:31, 14 February 2014
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	~~This is the main page for documentation about DOCK.~~		see [[Category:DOCK]]

	~~main software distribute site:~~
	~~[http://dock.compbio.ucsf.edu Dock web site]~~

	DOCK addresses the problem of "docking" molecules to each other. In general, "docking" is the identification of the low-energy binding modes of a small molecule, or ligand, within the active site of a macromolecule, or receptor, whose structure is known. A compound that interacts strongly with, or binds, a receptor associated with a disease may inhibit its function and thus act as a drug. Solving the docking problem computationally requires an accurate representation of the molecular energetics as well as an efficient algorithm to search the potential binding modes.

	Historically, the DOCK algorithm addressed rigid body docking using a geometric matching algorithm to superimpose the ligand onto a negative image of the binding pocket. Important features that improved the algorithm's ability to find the lowest-energy binding mode, including force-field based scoring, on-the-fly optimization, an improved matching algorithm for rigid body docking and an algorithm for flexible ligand docking, have been added over the years. For more information on past versions of DOCK, click here.

	With the release of DOCK 6, we continue to improve the algorithm's ability to predict binding poses by adding new features like force-field scoring enhanced by solvation and receptor flexibility. For more information about the current release of DOCK, click here.

	[[Category:DOCK]]

Therese: 4 revisions

2012-10-08T20:11:53Z

4 revisions

← Older revision

Revision as of 20:11, 8 October 2012

JohnIrwin at 18:35, 21 September 2007

2007-09-21T18:35:43Z

← Older revision		Revision as of 18:35, 21 September 2007
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	[http://dock.compbio.ucsf.edu Dock web site]		[http://dock.compbio.ucsf.edu Dock web site]

			DOCK addresses the problem of "docking" molecules to each other. In general, "docking" is the identification of the low-energy binding modes of a small molecule, or ligand, within the active site of a macromolecule, or receptor, whose structure is known. A compound that interacts strongly with, or binds, a receptor associated with a disease may inhibit its function and thus act as a drug. Solving the docking problem computationally requires an accurate representation of the molecular energetics as well as an efficient algorithm to search the potential binding modes.

			Historically, the DOCK algorithm addressed rigid body docking using a geometric matching algorithm to superimpose the ligand onto a negative image of the binding pocket. Important features that improved the algorithm's ability to find the lowest-energy binding mode, including force-field based scoring, on-the-fly optimization, an improved matching algorithm for rigid body docking and an algorithm for flexible ligand docking, have been added over the years. For more information on past versions of DOCK, click here.

	~~DOCK addresses~~ the ~~problem~~ of ~~"docking" molecules~~ to ~~each other. In general, "docking" is~~ the ~~identification of the low~~-~~energy binding modes of a small molecule, or ligand, within the active site of a macromolecule, or receptor, whose structure is known. A compound that interacts strongly with, or binds, a~~ receptor ~~associated with a disease may inhibit its function and thus act as a drug~~. ~~Solving~~ the ~~docking problem computationally requires an accurate representation~~ of ~~the molecular energetics as well as an efficient algorithm to search the potential binding modes~~.		With the release of DOCK 6, we continue to improve the algorithm's ability to predict binding poses by adding new features like force-field scoring enhanced by solvation and receptor flexibility. For more information about the current release of DOCK, click here.

	~~Historically, the~~ DOCK algorithm addressed rigid body docking using a geometric matching algorithm to superimpose the ligand onto a negative image of the binding pocket. Important features that improved the algorithm's ability to find the lowest-energy binding mode, including force-field based scoring, on-the-fly optimization, an improved matching algorithm for rigid body docking and an algorithm for flexible ligand docking, have been added over the years. For more information on past versions of DOCK, click here.		[[Category:DOCK]]

	With the release of DOCK 6, we continue to improve the algorithm's ability to predict binding poses by adding new features like force-field scoring enhanced by solvation and receptor flexibility. For more information about the current release of DOCK, click here.

JohnIrwin at 23:53, 19 September 2006

2006-09-19T23:53:43Z

← Older revision		Revision as of 23:53, 19 September 2006
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	main software distribute site:		main software distribute site:
	[http://dock.compbio.ucsf.edu Dock web site]		[http://dock.compbio.ucsf.edu Dock web site]



			DOCK addresses the problem of "docking" molecules to each other. In general, "docking" is the identification of the low-energy binding modes of a small molecule, or ligand, within the active site of a macromolecule, or receptor, whose structure is known. A compound that interacts strongly with, or binds, a receptor associated with a disease may inhibit its function and thus act as a drug. Solving the docking problem computationally requires an accurate representation of the molecular energetics as well as an efficient algorithm to search the potential binding modes.

			Historically, the DOCK algorithm addressed rigid body docking using a geometric matching algorithm to superimpose the ligand onto a negative image of the binding pocket. Important features that improved the algorithm's ability to find the lowest-energy binding mode, including force-field based scoring, on-the-fly optimization, an improved matching algorithm for rigid body docking and an algorithm for flexible ligand docking, have been added over the years. For more information on past versions of DOCK, click here.

			With the release of DOCK 6, we continue to improve the algorithm's ability to predict binding poses by adding new features like force-field scoring enhanced by solvation and receptor flexibility. For more information about the current release of DOCK, click here.

JohnIrwin at 23:29, 19 September 2006

2006-09-19T23:29:10Z

← Older revision		Revision as of 23:29, 19 September 2006
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	This is the main page for documentation about DOCK.		This is the main page for documentation about DOCK.

			main software distribute site:
			[http://dock.compbio.ucsf.edu Dock web site]

JohnIrwin at 22:18, 19 September 2006

2006-09-19T22:18:57Z

New page

This is the main page for documentation about DOCK.