DOCK 3: Difference between revisions

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DOCK 3 is the version of [[DOCK]] used, maintained and developed in the [[Shoichet Laboratory]].  It is the engine behind [[DOCK Blaster]] and the basis for all the docking work published from the lab.  For more information, please see the flyer [http://blaster.docking.org/WhyUseDOCK.pdf Why Use DOCK]].
DOCK 3 is the version of [[DOCK]] used, maintained and developed in the [[Shoichet Laboratory]].  It is the engine behind [[DOCK Blaster]] and the basis for all the docking work [http://www.bkslab.org/publications.php published from the lab].  For more information, please see the flyer [http://blaster.docking.org/WhyUseDOCK.pdf Why Use DOCK]].


For more information see the following:
The current distributed version of DOCK 3 is [[DOCK 3.7]].
*[[DOCK 3.6 User Manual]]  
[[DOCK Blaster]] still uses [[DOCK 3.6]], and we are actively working to change it over to DOCK 3.7. [[DOCK:History | The History of DOCK ]] helps explain why two versions of DOCK continue to be developed.
*[[DOCK 3.6]]
*[[BKS lab Structure preparation]]
 
= History =
* DOCK 3.0 was initially released in 1992 by the [[Kuntz Laboratory]].
* DOCK 3.5 was released in 1993.
* 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.
* DOCK 3.5 returned to [[UCSF]] in 2003 as [[DOCK 3.5.54]] when the [[Shoichet Laboratory]] moved there.
* DOCK 3.5.54 remained largely unchanged except for minor bugfixes from 2003-2008.
** Brian Shoichet wrote solvmap.
** Michael Mysinger wrote code to read gzipped database files.
** 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]].
 
* From 2008 - May 2010, a number of changes were made. These changes (below) were rolled up and called [[DOCK 3.6]] in May 2010.
** MMM improved handling of ligand desolvation maps
** 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.
* From May 2010 until the present (May 2011), more changes have been made, but have not yet been released.
* In September of 2013 [[DOCK 3.7]] was released, for details of the changes see [http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075992 coleman et al].


= Relationship to DOCK 6 =
= Relationship to DOCK 6 =
[[DOCK 6]] has the same goal as [[DOCK 3]], but it is a completely different program, with different inputs, outputs and algorithms.  
[[DOCK 6]] has the same goal as [[DOCK 3]], but it is a completely different program, with different inputs, outputs and algorithms.  


[[Category:DOCK]]
[[Category:DOCK]]
[[Category:Software]]

Latest revision as of 15:19, 12 March 2014

DOCK 3 is the version of DOCK used, maintained and developed in the Shoichet Laboratory. It is the engine behind DOCK Blaster and the basis for all the docking work published from the lab. For more information, please see the flyer Why Use DOCK].

The current distributed version of DOCK 3 is DOCK 3.7. DOCK Blaster still uses DOCK 3.6, and we are actively working to change it over to DOCK 3.7. The History of DOCK helps explain why two versions of DOCK continue to be developed.

Relationship to DOCK 6

DOCK 6 has the same goal as DOCK 3, but it is a completely different program, with different inputs, outputs and algorithms.

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