DOCK Blaster:History: Difference between revisions
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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 | * 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 | ||
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]]. | ||
| Line 19: | Line 19: | ||
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" | ||
| Line 29: | Line 30: | ||
* 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]] | [[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]] | ||
Latest revision as of 20:02, 8 October 2012
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 were not available
- metalloenzymes were problematic, ruling out perhaps 20% of biology.
- the method had many steps that still required animal sacrifices
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 near-automated docking
- 2003/06 DOCK Blaster with GUI starts to be used by members of the Shoichet Lab.
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.
- 2007/09 DOCK Blaster can "do DUD automatically"
- 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.
- 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.
- 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.