DOCK Blaster:History: Difference between revisions
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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 | * 2000/07 Preliminary work by [[John Irwin]] begins. | ||
* 2000 | * 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 | * 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 | * 2007/03 Alpha testing with 10+ users outside [[UCSF]]. | ||
* 2007 | * 2007/09 DOCK Blaster can "do DUD automatically" | ||
* 2007 | * 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 | * 2009/01 Number of users > 50 | ||
* 2009 [[Eddie Cao]] performs extensive testing. | * 2009 [[Eddie Cao]] performs extensive testing. | ||
* 2009 | * 2009/05 Manuscript submitted | ||
* 2009 | * 2009/08 Manuscript accepted, DOCK Blaster becomes public. | ||
* 2009 | * 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]] | ||
Revision as of 00:43, 7 August 2009
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 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.
- 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.
- 2000/07 Preliminary work by John Irwin begins.
- 2000/11 First MakeDOCK script by David M. Lorber in Brian Shoichet's lab.
- 2001 Further refinements to MakeDOCK by Binqing Wei
- 2002 Refinements and new contributions by Austin N. Kirschner
- 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
- 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).
- 2007/03 Alpha testing with 10+ users outside UCSF.
- 2007/09 DOCK Blaster can "do DUD automatically"
- 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.
- 2009/01 Number of users > 50
- 2009 Eddie Cao performs extensive testing.
- 2009/05 Manuscript submitted
- 2009/08 Manuscript accepted, DOCK Blaster becomes public.
- 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.