DUD - Revision history

Khtang at 20:44, 3 January 2019

2019-01-03T20:44:50Z

← Older revision		Revision as of 20:44, 3 January 2019
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	* A total of 2,950 active compounds against a total of 40 targets.		* A total of 2,950 active compounds against a total of 40 targets.
	* For each active, 36 "decoys" with similar physical properties (e.g. molecular weight, calculated LogP) but dissimilar topology.		* For each active, 36 "decoys" with similar physical properties (e.g. molecular weight, calculated LogP) but dissimilar topology.
	[http://wiki.docking.org/index.php/DUD#DUD-E \| DUDE] is the most current and upgrade of DUD.		[http://wiki.docking.org/index.php/DUD#DUD-E DUDE] is the most current and upgrade of DUD.
	==Cite DUD==		==Cite DUD==
	To cite DUD, please reference Huang, Shoichet and Irwin, J. Med. Chem., 2006, 49(23), 6789-6801. [http://pubs.acs.org/doi/abs/10.1021/jm0608356 DOI:10.1021/jm0608356]		To cite DUD, please reference Huang, Shoichet and Irwin, J. Med. Chem., 2006, 49(23), 6789-6801. [http://pubs.acs.org/doi/abs/10.1021/jm0608356 DOI:10.1021/jm0608356]

Khtang at 20:44, 3 January 2019

2019-01-03T20:44:40Z

← Older revision		Revision as of 20:44, 3 January 2019
Line 14:		Line 14:
	* A total of 2,950 active compounds against a total of 40 targets.		* A total of 2,950 active compounds against a total of 40 targets.
	* For each active, 36 "decoys" with similar physical properties (e.g. molecular weight, calculated LogP) but dissimilar topology.		* For each active, 36 "decoys" with similar physical properties (e.g. molecular weight, calculated LogP) but dissimilar topology.
	[[DUDE]] is the most current and upgrade of DUD.		[http://wiki.docking.org/index.php/DUD#DUD-E \| DUDE] is the most current and upgrade of DUD.
	==Cite DUD==		==Cite DUD==
	To cite DUD, please reference Huang, Shoichet and Irwin, J. Med. Chem., 2006, 49(23), 6789-6801. [http://pubs.acs.org/doi/abs/10.1021/jm0608356 DOI:10.1021/jm0608356]		To cite DUD, please reference Huang, Shoichet and Irwin, J. Med. Chem., 2006, 49(23), 6789-6801. [http://pubs.acs.org/doi/abs/10.1021/jm0608356 DOI:10.1021/jm0608356]

Khtang at 20:43, 3 January 2019

2019-01-03T20:43:26Z

← Older revision		Revision as of 20:43, 3 January 2019
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	\|Developer = [[Shoichet Lab]]		\|Developer = [[Shoichet Lab]]
	\|Stable Version = [[DUDE]]		\|Stable Version = [[DUDE]]
	\|Programming Language = [[Python]]		\|Programming Language = [[Python]], [[Perl]]
	\|Dependencies = [[JChem]], [[ChemAxon]]		\|Dependencies = [[JChem]], [[ChemAxon]]
	}}		}}

Khtang at 20:35, 3 January 2019

2019-01-03T20:35:26Z

← Older revision		Revision as of 20:35, 3 January 2019
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	~~'''DUD''' stands for "a '''D'''irectory of '''U'''seful '''D'''ecoys". DUD is designed to help test docking algorithms by providing challenging decoys.~~

	{{Software_Infobox		{{Software_Infobox
	\|title =		\|title = DUD
	\|image =		\|image = Dud.jpg
	\|Paragigm = [[Docking]]		\|Paragigm = [[Docking]]
	\|Developer = [[Shoichet Lab]]		\|Developer = [[Shoichet Lab]]
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	}}		}}

			'''DUD''' stands for "a '''D'''irectory of '''U'''seful '''D'''ecoys". DUD is designed to help test docking algorithms by providing challenging decoys.
	==About==		==About==
	DUD is drawn from [[ZINC]], a database of commerically available compounds for virtual screening, so compounds in DUD are purchasable, although some may become depleted over time. It contains:		DUD is drawn from [[ZINC]], a database of commerically available compounds for virtual screening, so compounds in DUD are purchasable, although some may become depleted over time. It contains:

Khtang at 20:27, 3 January 2019

2019-01-03T20:27:06Z

← Older revision		Revision as of 20:27, 3 January 2019
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	'''DUD''' stands for "a '''D'''irectory of '''U'''seful '''D'''ecoys". DUD is designed to help test docking algorithms by providing challenging decoys.		'''DUD''' stands for "a '''D'''irectory of '''U'''seful '''D'''ecoys". DUD is designed to help test docking algorithms by providing challenging decoys.

			{{Software_Infobox
			\|title =
			\|image =
			\|Paragigm = [[Docking]]
			\|Developer = [[Shoichet Lab]]
			\|Stable Version = [[DUDE]]
			\|Programming Language = [[Python]]
			\|Dependencies = [[JChem]], [[ChemAxon]]
			}}

	==About==		==About==

Khtang at 22:33, 20 December 2018

2018-12-20T22:33:35Z

← Older revision		Revision as of 22:33, 20 December 2018
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	[http://dud.docking.org/ DUD Web Site]		[http://dud.docking.org/ DUD Web Site]

	==~~DUDE~~==		==DUD-E==
	[[DUDE]] is a Directory of Useful Decoys - Enhanced and is DUD's descendent.		[[DUDE]] is a Directory of Useful Decoys - Enhanced and is DUD's descendent.

Khtang at 21:38, 20 December 2018

2018-12-20T21:38:02Z

← Older revision		Revision as of 21:38, 20 December 2018
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	==About==		==About==
	~~We think~~ DUD ~~might be useful as part of a~~ [[~~Docking Competition~~]]~~. This wiki page~~ may ~~be used to discuss DUD and to report results~~. ~~We welcome all helpful feedback~~. ~~If you find problems~~ with ~~DUD, please tell John Irwin~~, but ~~you may also want to point out these problems here~~. ~~This~~ is ~~really a forum for~~ DUD ~~users to share their experiences~~.		DUD is drawn from [[ZINC]], a database of commerically available compounds for virtual screening, so compounds in DUD are purchasable, although some may become depleted over time. It contains:
			* A total of 2,950 active compounds against a total of 40 targets.
	[http://~~dud~~.~~docking~~.org/ ~~DUD Web Site~~]		* For each active, 36 "decoys" with similar physical properties (e.g. molecular weight, calculated LogP) but dissimilar topology.
			[[DUDE]] is the most current and upgrade of DUD.
			==Cite DUD==
			To cite DUD, please reference Huang, Shoichet and Irwin, J. Med. Chem., 2006, 49(23), 6789-6801. [http://pubs.acs.org/doi/abs/10.1021/jm0608356 DOI:10.1021/jm0608356]
	==Version Released==		==Version Released==
	{\| class="wikitable"		{\| class="wikitable"
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	the final manuscript		the final manuscript
	\|}		\|}
	==~~Cite DUD~~==		==Quick Note==
	~~To cite~~ DUD, please ~~reference Huang, Shoichet and~~ Irwin, J. ~~Med. Chem., 2006, 49(23), 6789-6801~~. [http://~~pubs~~.~~acs~~.org/~~doi/abs/10.1021/jm0608356 DOI:10.1021/jm0608356~~]		We think DUD might be useful as part of a [[Docking Competition]]. This wiki page may be used to discuss DUD and to report results. We welcome all helpful feedback. If you find problems with DUD, please tell John Irwin, but you may also want to point out these problems here. This is really a forum for DUD users to share their experiences.

			[http://dud.docking.org/ DUD Web Site]

	==DUDE==		==DUDE==
	[[DUDE]] is a Directory of Useful Decoys - Enhanced and is DUD's descendent.		[[DUDE]] is a Directory of Useful Decoys - Enhanced and is DUD's descendent.

Khtang at 20:14, 20 December 2018

2018-12-20T20:14:54Z

← Older revision		Revision as of 20:14, 20 December 2018
Line 1:		Line 1:
			'''DUD''' stands for "a '''D'''irectory of '''U'''seful '''D'''ecoys". DUD is designed to help test docking algorithms by providing challenging decoys.

	==About==		==About==
	~~'''DUD''' stands for "a '''D'''irectory of '''U'''seful '''D'''ecoys". DUD is designed to help test docking algorithms by providing challenging decoys.~~ We think DUD might be useful as part of a [[Docking Competition]]. This wiki page may be used to discuss DUD and to report results. We welcome all helpful feedback. If you find problems with DUD, please tell John Irwin, but you may also want to point out these problems here. This is really a forum for DUD users to share their experiences.		We think DUD might be useful as part of a [[Docking Competition]]. This wiki page may be used to discuss DUD and to report results. We welcome all helpful feedback. If you find problems with DUD, please tell John Irwin, but you may also want to point out these problems here. This is really a forum for DUD users to share their experiences.

	[http://dud.docking.org/ DUD Web Site]		[http://dud.docking.org/ DUD Web Site]

Khtang at 20:14, 20 December 2018

2018-12-20T20:14:20Z

← Older revision		Revision as of 20:14, 20 December 2018
Line 1:		Line 1:
	~~A directory~~ of ~~universal decoys (DUD)~~. ~~The~~ DUD ~~paper was published in J Med Chem, appearing on ASAP October 25-26th~~. We think DUD might be useful as part of a [[Docking Competition]]. This wiki page may be used to discuss DUD and to report results. We welcome all helpful feedback. If you find problems with DUD, please tell John Irwin, but you may also want to point out these problems here. This is really a forum for DUD users to share their experiences.		==About==
			'''DUD''' stands for "a '''D'''irectory of '''U'''seful '''D'''ecoys". DUD is designed to help test docking algorithms by providing challenging decoys. We think DUD might be useful as part of a [[Docking Competition]]. This wiki page may be used to discuss DUD and to report results. We welcome all helpful feedback. If you find problems with DUD, please tell John Irwin, but you may also want to point out these problems here. This is really a forum for DUD users to share their experiences.

	[http://dud.docking.org/ DUD Web Site]		[http://dud.docking.org/ DUD Web Site]

	[http://dx.~~doi~~.org/10.1021/jm0608356 DOI 10.1021/~~jm068356~~]		==Version Released==
			{\| class="wikitable"
			\|-
			! scope="col" \| Release
			! scope="col" \| Date
			! scope="col" \| Comment
			\|-
			! scope="row" \| 1
			\| Oct 1, 2006
			\|Original release
			\|-
			! scope="row" \| 2
			\| Oct 22, 2006
			\| Proofreading corrections accompanying
			the final manuscript
			\|}
			==Cite DUD==
			To cite DUD, please reference Huang, Shoichet and Irwin, J. Med. Chem., 2006, 49(23), 6789-6801. [http://pubs.acs.org/doi/abs/10.1021/jm0608356 DOI:10.1021/jm0608356]
	==DUDE==		==DUDE==
			[[DUDE]] is a Directory of Useful Decoys - Enhanced and is DUD's descendent.
	[[DUDE]] is a ~~directory~~ of ~~useful decoys~~ - ~~enhanced~~ and is DUD's ~~decendent~~.

	[http://dude.docking.org DUDE Web Site]		[http://dude.docking.org DUDE Web Site]

Frodo at 04:19, 13 March 2014

2014-03-13T04:19:16Z

← Older revision		Revision as of 04:19, 13 March 2014
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	[[Category:Data]]		[[Category:Data]]
	[[Category:Websites]]		[[Category:Websites]]
			[[Category:Decoys]]