DOCK:History - Revision history

Frodo: /* Version 6.9 - circa 2020 - present */ asdf

2025-08-05T23:06:56Z

Version 6.9 - circa 2020 - present: asdf

@@ Line 135: / Line 135: @@
 * amber_score as secondary score currently deprecated
-DOCK 6.9 is under active development in the lab of Robert Rizzo at SUNY Stony Brook with help from investigators at other sites.
 [[Category:DOCK]]
 [[Category:History]]

Frodo: /* Version 3.6 - circa 2010 to present */

2021-01-27T17:01:48Z

Version 3.6 - circa 2010 to present

← Older revision		Revision as of 17:01, 27 January 2021
Line 49:		Line 49:
	* Niu Huang wrote flexible water handling code, based on BinQing Wei's flexible receptor code. This has not been incorporated into the germ line version of [[DOCK 3]].		* Niu Huang wrote flexible water handling code, based on BinQing Wei's flexible receptor code. This has not been incorporated into the germ line version of [[DOCK 3]].

	= Version 3.6 - ~~circa~~ 2010 to ~~present~~ =		= Version 3.6 - 2010 to 2015 =
	Authors: Michael Mysinger, Michael Carchia, Ryan Coleman, Brian Shoichet		Authors: Michael Mysinger, Michael Carchia, Ryan Coleman, Brian Shoichet

Line 56:		Line 56:
	* Mike Carchia speeded up the already fast code from 3X to 5X using compiler optimizations, data duplication, and other techniques.		* Mike Carchia speeded up the already fast code from 3X to 5X using compiler optimizations, data duplication, and other techniques.
	* Ryan Coleman improved the handling of ligand hierarchies by improving the algorithms in mol2db and dock for sampling ligands. Additional work was put into clash-checking ligands, checking to make sure the ligands do not fall outside of the grid boundaries, and general code cleanup.		* Ryan Coleman improved the handling of ligand hierarchies by improving the algorithms in mol2db and dock for sampling ligands. Additional work was put into clash-checking ligands, checking to make sure the ligands do not fall outside of the grid boundaries, and general code cleanup.

			There was overlap between 3.6 and 3.7. They were both used in 2013, 2014, 2015.

	= Version 3.7 - 2013 to 2021 =		= Version 3.7 - 2013 to 2021 =

Frodo: /* Version 6.9 - circa 2020 - present */

2021-01-27T17:00:58Z

Version 6.9 - circa 2020 - present

← Older revision		Revision as of 17:00, 27 January 2021
Line 133:		Line 133:
	* amber_score as secondary score currently deprecated		* amber_score as secondary score currently deprecated

			DOCK 6.9 is under active development in the lab of Robert Rizzo at SUNY Stony Brook with help from investigators at other sites.

	[[Category:DOCK]]		[[Category:DOCK]]
	[[Category:History]]		[[Category:History]]

Frodo: /* Version 6.5 - circa 2011 - 2012 */

2021-01-27T16:59:58Z

Version 6.5 - circa 2011 - 2012

← Older revision		Revision as of 16:59, 27 January 2021
Line 102:		Line 102:


	== Version 6.5 - circa 2011 - 2012 ==		== Version 6.5 - circa 2011 - 2012 ==

			* new anchor controls
			* new scoring functions
			* AMBER score improvements
			* PB/SA score improvements

	== Version 6.6 - circa 2012 - 2014 ==		== Version 6.6 - circa 2012 - 2014 ==

Frodo: /* Version 6.6 - circa 2012 - 2014 */

2021-01-27T16:59:07Z

Version 6.6 - circa 2012 - 2014

← Older revision		Revision as of 16:59, 27 January 2021
Line 105:		Line 105:


	== Version 6.6 - circa 2012 - 2014 ==		== Version 6.6 - circa 2012 - 2014 ==

			* new scoring function
			* orienting improvements
			* Hungarian RMSD

	== Version 6.7 - circa 2014 - 2017 ==		== Version 6.7 - circa 2014 - 2017 ==

Frodo: /* Version 6.7 - circa 2014 - present */

2021-01-27T16:58:14Z

Version 6.7 - circa 2014 - present

@@ Line 107: / Line 107: @@
 == Version 6.6 - circa 2012 - 2014 ==
-== Version 6.7 - circa 2014 - present ==
+== Version 6.7 - circa 2014 - 2017 ==
 [[Category:DOCK]]
 [[Category:History]]

Frodo: /* Version 3.7 - circa 2013 to present */

2021-01-27T16:52:38Z

Version 3.7 - circa 2013 to present

← Older revision		Revision as of 16:52, 27 January 2021
Line 57:		Line 57:
	* Ryan Coleman improved the handling of ligand hierarchies by improving the algorithms in mol2db and dock for sampling ligands. Additional work was put into clash-checking ligands, checking to make sure the ligands do not fall outside of the grid boundaries, and general code cleanup.		* Ryan Coleman improved the handling of ligand hierarchies by improving the algorithms in mol2db and dock for sampling ligands. Additional work was put into clash-checking ligands, checking to make sure the ligands do not fall outside of the grid boundaries, and general code cleanup.

	= Version 3.7 - ~~circa~~ 2013 to ~~present~~ =		= Version 3.7 - 2013 to 2021 =
	Major author: Ryan Coleman		Major author: Ryan Coleman
	Paper: [http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075992 coleman et al].		Paper: [http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075992 coleman et al].

	[[DOCK 3.7]] is the ~~current~~ version of the [[DOCK 3]] series of docking programs. It was released in 2013.		[[DOCK 3.7]] was the main version in the [[DOCK 3]] series of docking programs for 8 years. It was released in 2013.

	The current status of the DOCK 3.X series is that DOCK 3.7 is ~~being tested,~~ and ~~that~~ DOCK 3.6 will eventually be retired. At the moment (~~Spring 2015~~), both versions ~~of the code~~ are in use in the lab.		The current status of the DOCK 3.X series is that DOCK 3.7 is used in production and DOCK 3.8 will start taking over in 2021. DOCK 3.7 will eventually be retired. At the moment (Jan 2021), both versions are in use in the lab, but DOCK 3.7 is favored. That should reverse by May.
			DOCK 3.7 works with ZINC15/20. It will read ZINC22 but cannot do the strain calculation.

			= Version 3.8 - 2021 to present =
			Major contributors: Jiankun Lyu, Trent Balius, Ben Tingle

			[[DOCK 3.8]] is the current development branch in the lab. It builds on DOCK 3.7 and contains three innovations:
			* an internal strain energy calculation is now built into the database [[ZINC22]] and used in the DOCK score
			* many new scripts have been added or extended to simplify the process
			* DOCK 3.8 can be interrupted and restarted, allowing it to be used more efficiently on AWS and shared clusters.
			* DOCK 3.8 can read both ZINC22 and ZINC15/20 databases.

	= DOCK 4 Series =		= DOCK 4 Series =

Frodo: spring 2015 refresh

2015-04-15T16:32:16Z

spring 2015 refresh

← Older revision		Revision as of 16:32, 15 April 2015
Line 18:		Line 18:

	= DOCK 3 Series =		= DOCK 3 Series =
	The DOCK 3 Series is coded mostly in Fortran, with ~~come~~ C.		The DOCK 3 Series is coded mostly in Fortran, with some C.

	== Version 3.0 - circa 1992 - 1994 ==		== Version 3.0 - circa 1992 - 1994 ==
Line 34:		Line 34:
	* critical clustering.		* critical clustering.

	== Version 3.5.54 ==		== Version 3.5.54 - circa 1998 - 2010 ==
	Authors: David M. Lorber and Brian K. Shoichet		Authors: David M. Lorber and Brian K. Shoichet

	From 1994-2002, DOCK 3.5 was developed in the group of Brian Shoichet, first at the University of Oregon, then at Northwestern University Medical School. The major author of the changes was David Lorber. BinQing Wei and other lab members also contributed.		From 1994-2002, DOCK 3.5 was developed in the group of Brian Shoichet, first at the University of Oregon, then at Northwestern University Medical School, then at UCSF. The major author of the changes was David Lorber. BinQing Wei and other lab members also contributed.

	The main innovations were:		The main innovations were:
Line 49:		Line 49:
	* Niu Huang wrote flexible water handling code, based on BinQing Wei's flexible receptor code. This has not been incorporated into the germ line version of [[DOCK 3]].		* Niu Huang wrote flexible water handling code, based on BinQing Wei's flexible receptor code. This has not been incorporated into the germ line version of [[DOCK 3]].

	= Version 3.6 =		= Version 3.6 - circa 2010 to present =
	Authors: Michael Mysinger, Michael Carchia, Ryan Coleman, Brian Shoichet		Authors: Michael Mysinger, Michael Carchia, Ryan Coleman, Brian Shoichet

Line 57:		Line 57:
	* Ryan Coleman improved the handling of ligand hierarchies by improving the algorithms in mol2db and dock for sampling ligands. Additional work was put into clash-checking ligands, checking to make sure the ligands do not fall outside of the grid boundaries, and general code cleanup.		* Ryan Coleman improved the handling of ligand hierarchies by improving the algorithms in mol2db and dock for sampling ligands. Additional work was put into clash-checking ligands, checking to make sure the ligands do not fall outside of the grid boundaries, and general code cleanup.

	= Version 3.7 =		= Version 3.7 - circa 2013 to present =
	Major author: Ryan Coleman		Major author: Ryan Coleman
	Paper: [http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075992 coleman et al].		Paper: [http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075992 coleman et al].

	[[DOCK 3.7]] is the current version of the [[DOCK 3]] series of docking programs. It was released in 2013.		[[DOCK 3.7]] is the current version of the [[DOCK 3]] series of docking programs. It was released in 2013.

			The current status of the DOCK 3.X series is that DOCK 3.7 is being tested, and that DOCK 3.6 will eventually be retired. At the moment (Spring 2015), both versions of the code are in use in the lab.

	= DOCK 4 Series =		= DOCK 4 Series =
Line 76:		Line 78:
	Authors: Demetri Moustakas, P. Therese Lang, Scott Pegg, Scott Brozell, Irwin Kuntz		Authors: Demetri Moustakas, P. Therese Lang, Scott Pegg, Scott Brozell, Irwin Kuntz

	Version 5 was rewritten in C++ in a modular format, which allows for easy implementation of new scoring functions, sampling methods and analysis tools (Moustakas, et al, 2006). Additional new features include MPI parallelization, exhaustive orientation searching, improved conformation searching, GB/SA solvation scoring, and post-screening pose clustering. (Zou, et al. J. Am. Chem. Soc., 1999)		Version 5 was rewritten in C++ in a modular format, which allows for easy implementation of new scoring functions, sampling methods and analysis tools (Moustakas, et al, 2006). Additional new features include MPI parallelization, exhaustive orientation searching, improved conformation searching, GB/SA solvation scoring, and post-screening pose clustering. (Zou, et al. J. Am. Chem. Soc., 1999). DOCK 5 is entirely superseded by DOCK 6.

	== Version 6.0 - circa 2006 - 2007 ==		== Version 6.0 - circa 2006 - 2007 ==
Line 82:		Line 84:
	[[DOCK 6]] is an extension of the [[DOCK 5]] code base. It includes the implementation of Hawkins-Cramer-Truhlar GB/SA solvation scoring with salt screening and PB/SA solvation scoring through OpenEye's Zap Library. Additional flexibility has been added to scoring options during minimization. The new code also incorporates [[DOCK 3.5.54]] scoring features like [[Delphi]] electrostatics, [[ligand desolvation]], and [[receptor desolvation]]. Finally, [[DOCK 6]] introduces new code that allows access to the NAB library of functions such as receptor flexibility, the full [[AMBER]] molecular mechanics scoring function with implicit solvent, conjugate gradient minimization, and molecular dynamics simulation capabilities.		[[DOCK 6]] is an extension of the [[DOCK 5]] code base. It includes the implementation of Hawkins-Cramer-Truhlar GB/SA solvation scoring with salt screening and PB/SA solvation scoring through OpenEye's Zap Library. Additional flexibility has been added to scoring options during minimization. The new code also incorporates [[DOCK 3.5.54]] scoring features like [[Delphi]] electrostatics, [[ligand desolvation]], and [[receptor desolvation]]. Finally, [[DOCK 6]] introduces new code that allows access to the NAB library of functions such as receptor flexibility, the full [[AMBER]] molecular mechanics scoring function with implicit solvent, conjugate gradient minimization, and molecular dynamics simulation capabilities.

	Versions 6.1, 6.2, 6.3 were released, but they all had significant ~~problems~~.		Versions 6.1, 6.2, 6.3 were released, but they all had significant liabilities.

	== Version 6.4 - circa 2010 - 2011 ==		== Version 6.4 - circa 2010 - 2011 ==
Line 93:		Line 95:


	== Version 6.6 - circa 2012 - present ==		== Version 6.6 - circa 2012 - 2014 ==

			== Version 6.7 - circa 2014 - present ==


	[[Category:DOCK]]		[[Category:DOCK]]
	[[Category:History]]		[[Category:History]]

Frodo at 18:35, 15 February 2014

2014-02-15T18:35:46Z

Show changes

Frodo: /* Version 3.7 */

2014-02-15T18:16:30Z

Version 3.7

← Older revision		Revision as of 18:16, 15 February 2014
Line 64:		Line 64:
	= Version 3.7 =		= Version 3.7 =

	[[DOCK 3.7]], a new version of the [[DOCK 3]] series of docking programs, ~~will appear~~ in ~~2012. The features and date have not been announced~~.		[[DOCK 3.7]], a new version of the [[DOCK 3]] series of docking programs, was released in 2013.

	[[Category:DOCK]]		[[Category:DOCK]]
	[[Category:History]]		[[Category:History]]