DOCK Blaster:History - Revision history

Therese: 13 revisions

2012-10-08T20:02:08Z

13 revisions

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Revision as of 20:02, 8 October 2012

Frodo at 17:17, 13 March 2012

2012-03-13T17:17:16Z

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	* 2010/1/1 Planned start on DOCK Blaster version 2, maybe.		* 2010/1/1 Planned start on DOCK Blaster version 2, maybe.

	[[DOCK Blaster]] would not be what it is, or ready when it is, without the work of the people mentioned above, and also the patient testing by lab members. Thank you to you all. Of course, any problems with [[DOCK Blaster]] are entirely the responsibility of [[John Irwin]]~~, who just left on a one way trip to Argentina~~.		[[DOCK Blaster]] would not be what it is, or ready when it is, without the work of the people mentioned above, and also the patient testing by lab members. Thank you to you all. Of course, any problems with [[DOCK Blaster]] are entirely the responsibility of [[John Irwin]].

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

Frodo at 04:41, 21 August 2009

2009-08-21T04:41:05Z

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	* 2009/08 Manuscript accepted, DOCK Blaster becomes public.		* 2009/08 Manuscript accepted, DOCK Blaster becomes public.
	* 2009/09 Manuscript published.		* 2009/09 Manuscript published.
			* 2009/9/9 Planned party
			* 2010/1/1 Planned start on DOCK Blaster version 2, maybe.

	[[DOCK Blaster]] would not be what it is, or ready when it is, without the work of the people mentioned above, and also the patient testing by lab members. Thank you to you all. Of course, any problems with [[DOCK Blaster]] are entirely the responsibility of [[John Irwin]], who just left on a one way trip to Argentina.		[[DOCK Blaster]] would not be what it is, or ready when it is, without the work of the people mentioned above, and also the patient testing by lab members. Thank you to you all. Of course, any problems with [[DOCK Blaster]] are entirely the responsibility of [[John Irwin]], who just left on a one way trip to Argentina.

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

Frodo at 00:51, 7 August 2009

2009-08-07T00:51:05Z

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	The idea of fully automated docking with [[DOCK Blaster]] has its origins in a conversation between [[Brian Shoichet]] and [[John Irwin]] around November 1999. Work on [[DOCK Blaster]] began in July 2000 when [[John Irwin]] arrived at Northwestern. It got off to a pretty slow start when it was realized that		The idea of fully automated docking with [[DOCK Blaster]] has its origins in a conversation between [[Brian Shoichet]] and [[John Irwin]] around November 1999. Work on [[DOCK Blaster]] began in July 2000 when [[John Irwin]] arrived at Northwestern. It got off to a pretty slow start when it was realized that

	* the basic benchmarking data necessary to even test such a method ~~was~~ not available		* the basic benchmarking data necessary to even test such a method were not available
			* metalloenzymes were problematic, ruling out perhaps 20% of biology.
	* the method had many steps that still required animal sacrifices		* the method had many steps that still required animal sacrifices
	* metalloenzymes were problematic, ruling out perhaps 20% of biology.

	Here are some of the people, events and times that contributed to [[DOCK Blaster]].		Here are some of the people, events and times that contributed to [[DOCK Blaster]].

Frodo at 00:48, 7 August 2009

2009-08-07T00:48:11Z

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	The [[DUD]] paper (Huang, Shoichet, Irwin J Med Chem, 2006) started out being the [[DOCK Blaster]] paper. When [[DUD]] was released, it was really the end of the beginning, because [[DUD]] had forced us finish nearly all the steps of the automation (except for starting from a [[PDB]] code).		The [[DUD]] paper (Huang, Shoichet, Irwin J Med Chem, 2006) started out being the [[DOCK Blaster]] paper. When [[DUD]] was released, it was really the end of the beginning, because [[DUD]] had forced us finish nearly all the steps of the automation (except for starting from a [[PDB]] code).

			* 2007/01 [[Pascal Wassam]] joins as system manager, upgrades the cluster from a VW Bus to a BMW.
	* 2007/03 Alpha testing with 10+ users outside [[UCSF]].		* 2007/03 Alpha testing with 10+ users outside [[UCSF]].
	* 2007/09 [[DOCK Blaster]] can "do DUD automatically"		* 2007/09 [[DOCK Blaster]] can "do DUD automatically"

Frodo at 00:45, 7 August 2009

2009-08-07T00:45:48Z

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	* 2003/06 DOCK Blaster with GUI starts to be used by members of the [[Shoichet Lab]].		* 2003/06 DOCK Blaster with GUI starts to be used by members of the [[Shoichet Lab]].

	The [[DUD]] paper (Huang, J Med Chem, 2006) started out being the DOCK Blaster paper. When [[DUD]] was released, it was really the end of the beginning, because DUD had forced us finish nearly all the steps of the automation (except for starting from a PDB code).		The [[DUD]] paper (Huang, Shoichet, Irwin J Med Chem, 2006) started out being the [[DOCK Blaster]] paper. When [[DUD]] was released, it was really the end of the beginning, because [[DUD]] had forced us finish nearly all the steps of the automation (except for starting from a [[PDB]] code).

	* 2007/03 Alpha testing with 10+ users outside [[UCSF]].		* 2007/03 Alpha testing with 10+ users outside [[UCSF]].
	* 2007/09 DOCK Blaster can "do DUD automatically"		* 2007/09 [[DOCK Blaster]] can "do DUD automatically"
	* 2007/10 Beta testing with 30+ users outside [[UCSF]].		* 2007/10 Beta testing with 30+ users outside [[UCSF]].
	* 2008 [[Michael Mysinger]] makes numerous contributions, particularly to decoy generation.		* 2008 [[Michael Mysinger]] makes numerous contributions, particularly to decoy generation.

Frodo at 00:45, 7 August 2009

2009-08-07T00:45:02Z

← Older revision		Revision as of 00:45, 7 August 2009
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	* 2002 Refinements and new contributions by [[Austin N. Kirschner]]		* 2002 Refinements and new contributions by [[Austin N. Kirschner]]
	* 2003 [[ZINC]] is created by [[John Irwin]] as a necessary tool for [[DOCK Blaster]].		* 2003 [[ZINC]] is created by [[John Irwin]] as a necessary tool for [[DOCK Blaster]].
	* 2004-2006 [[Niu Huang]]'s work on [[DUD]] was the first real test of ~~semi~~-automated docking		* 2004-2006 [[Niu Huang]]'s work on [[DUD]] was the first real test of near-automated docking
	* 2003/06 DOCK Blaster with GUI starts to be used by members of the [[Shoichet Lab]].		* 2003/06 DOCK Blaster with GUI starts to be used by members of the [[Shoichet Lab]].

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	* 2007/09 DOCK Blaster can "do DUD automatically"		* 2007/09 DOCK Blaster can "do DUD automatically"
	* 2007/10 Beta testing with 30+ users outside [[UCSF]].		* 2007/10 Beta testing with 30+ users outside [[UCSF]].
			* 2008 [[Michael Mysinger]] makes numerous contributions, particularly to decoy generation.
	* 2008 [[Francesco Colizzi]] develops "be_blasti" and "auto_dock" enabling docking from a PDB code alone.		* 2008 [[Francesco Colizzi]] develops "be_blasti" and "auto_dock" enabling docking from a PDB code alone.
	* 2009/01 Number of users > 50		* 2009/01 Number of users > 50

Frodo at 00:44, 7 August 2009

2009-08-07T00:44:01Z

← Older revision		Revision as of 00:44, 7 August 2009
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	* 2002 Refinements and new contributions by [[Austin N. Kirschner]]		* 2002 Refinements and new contributions by [[Austin N. Kirschner]]
	* 2003 [[ZINC]] is created by [[John Irwin]] as a necessary tool for [[DOCK Blaster]].		* 2003 [[ZINC]] is created by [[John Irwin]] as a necessary tool for [[DOCK Blaster]].
	* 2004-2006 [[Niu Huang]]'s work on DUD was the first real test of semi-automated docking		* 2004-2006 [[Niu Huang]]'s work on [[DUD]] was the first real test of semi-automated docking
	* 2003/06 DOCK Blaster with GUI starts to be used by members of the [[Shoichet Lab]].		* 2003/06 DOCK Blaster with GUI starts to be used by members of the [[Shoichet Lab]].

Frodo at 00:43, 7 August 2009

2009-08-07T00:43:48Z

← Older revision		Revision as of 00:43, 7 August 2009
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	* 2001 Further refinements to MakeDOCK by [[Binqing Wei]]		* 2001 Further refinements to MakeDOCK by [[Binqing Wei]]
	* 2002 Refinements and new contributions by [[Austin N. Kirschner]]		* 2002 Refinements and new contributions by [[Austin N. Kirschner]]
	* 2003 ZINC is created by [[John Irwin]] as a necessary tool for [[DOCK Blaster]].		* 2003 [[ZINC]] is created by [[John Irwin]] as a necessary tool for [[DOCK Blaster]].
	* 2004-2006 [[Niu Huang]]'s work on DUD was the first real test of semi-automated docking		* 2004-2006 [[Niu Huang]]'s work on DUD was the first real test of semi-automated docking
	* 2003/06 DOCK Blaster with GUI starts to be used by members of the [[Shoichet Lab]].		* 2003/06 DOCK Blaster with GUI starts to be used by members of the [[Shoichet Lab]].

Frodo at 00:43, 7 August 2009

2009-08-07T00:43:17Z

← Older revision		Revision as of 00:43, 7 August 2009
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	* 1982-1993: DOCK Blaster draws heavily upon the manual docking protocol developed in [[Tack Kuntz]]'s lab.		* 1982-1993: DOCK Blaster draws heavily upon the manual docking protocol developed in [[Tack Kuntz]]'s lab.
	* 1989-2000 Further refinements of the manual protocol in [[Brian Shoichet]]'s lab.		* 1989-2000 Further refinements of the manual protocol in [[Brian Shoichet]]'s lab.
	* 2000-07 Preliminary work by [[John Irwin]] begins.		* 2000/07 Preliminary work by [[John Irwin]] begins.
	* 2000-11 First MakeDOCK script by [[David M. Lorber]] in [[Brian Shoichet]]'s lab.		* 2000/11 First MakeDOCK script by [[David M. Lorber]] in [[Brian Shoichet]]'s lab.
	* 2001 Further refinements to MakeDOCK by [[Binqing Wei]]		* 2001 Further refinements to MakeDOCK by [[Binqing Wei]]
	* 2002 Refinements and new contributions by [[Austin N. Kirschner]]		* 2002 Refinements and new contributions by [[Austin N. Kirschner]]
	* 2003 ZINC is created by [[John Irwin]] as a necessary tool for [[DOCK Blaster]].		* 2003 ZINC is created by [[John Irwin]] as a necessary tool for [[DOCK Blaster]].
	* 2004-2006 [[Niu Huang]]'s work on DUD was the first real test of semi-automated docking		* 2004-2006 [[Niu Huang]]'s work on DUD was the first real test of semi-automated docking
	* 2003-06 DOCK Blaster with GUI starts to be used by members of the [[Shoichet Lab]].		* 2003/06 DOCK Blaster with GUI starts to be used by members of the [[Shoichet Lab]].

	The [[DUD]] paper (Huang, J Med Chem, 2006) started out being the DOCK Blaster paper. When [[DUD]] was released, it was really the end of the beginning, because DUD had forced us finish nearly all the steps of the automation (except for starting from a PDB code).		The [[DUD]] paper (Huang, J Med Chem, 2006) started out being the DOCK Blaster paper. When [[DUD]] was released, it was really the end of the beginning, because DUD had forced us finish nearly all the steps of the automation (except for starting from a PDB code).

	* 2007-03 Alpha testing with 10+ users outside [[UCSF]].		* 2007/03 Alpha testing with 10+ users outside [[UCSF]].
	* 2007-09 DOCK Blaster can "do DUD automatically"		* 2007/09 DOCK Blaster can "do DUD automatically"
	* 2007-10 Beta testing with 30+ users outside [[UCSF]].		* 2007/10 Beta testing with 30+ users outside [[UCSF]].
	* 2008 [[Francesco Colizzi]] develops "be_blasti" and "auto_dock" enabling docking from a PDB code alone.		* 2008 [[Francesco Colizzi]] develops "be_blasti" and "auto_dock" enabling docking from a PDB code alone.
	* 2009-01 Number of users > 50		* 2009/01 Number of users > 50
	* 2009 [[Eddie Cao]] performs extensive testing.		* 2009 [[Eddie Cao]] performs extensive testing.
	* 2009-05 Manuscript submitted		* 2009/05 Manuscript submitted
	* 2009-08 Manuscript accepted, DOCK Blaster becomes public.		* 2009/08 Manuscript accepted, DOCK Blaster becomes public.
	* 2009-09 Manuscript published.		* 2009/09 Manuscript published.

	[[DOCK Blaster]] would not be what it is, or ready when it is, without the work of the people mentioned above, and also the patient testing by lab members. Thank you to you all. Of course, any problems with [[DOCK Blaster]] are entirely the responsibility of [[John Irwin]], who just left on a one way trip to Argentina.		[[DOCK Blaster]] would not be what it is, or ready when it is, without the work of the people mentioned above, and also the patient testing by lab members. Thank you to you all. Of course, any problems with [[DOCK Blaster]] are entirely the responsibility of [[John Irwin]], who just left on a one way trip to Argentina.

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