DOCK 3.6: Difference between revisions

From DISI
Jump to navigation Jump to search
m (24 revisions)
No edit summary
Line 1: Line 1:
DOCK 3.5.54 is a version of [[UCSF]] [[DOCK 3]] that was used, developed and maintained by the [[Shoichet Lab]] from 1998 to May 2010. All docking papers from the Shoichet Lab during that time used this program.  It was also used by [[DOCK Blaster]] until May 2010.  
DOCK 3.6 was the primary version of DOCK used in the [Shoichet Lab]] between 1998 and 2013.  It was also called DOCK 3.5.54 or even DOCK 3.5.5.4 or DOCK 3.5ens. It has been largely superseded by [[DOCK 3.7]].   All docking papers from the Shoichet Lab during that time used this program.  It was also used by [[DOCK Blaster]] from 2007 until present.  We intend to switch over to DOCK 3.7 during 2014.


DOCK 3.5.54 was superseded by [[DOCK 3.6]] in May 2010.  DOCK 3.5.54 is no longer available.
DOCK 3.5.54 was superseded by [[DOCK 3.6]] in May 2010.  DOCK 3.5.54 is no longer available.
Line 11: Line 11:


* [[INDOCK_for_DOCK_3.6]]
* [[INDOCK_for_DOCK_3.6]]
DOCK 3.6 is the current version of the [[DOCK 3]] series of docking programs used and developed in the [[Shoichet Lab]].  DOCK 3.6 is the engine used by [[DOCK Blaster]]. A sample [[INDOCK for DOCK 3.6]] is available.


= Release Date =  
= Release Date =  
DOCK 3.6 was released on April 31, 2010.
DOCK 3.6 was released on April 31, 2010.  


{{TOCright}}
{{TOCright}}
Line 49: Line 47:


[[Category:Software]]
[[Category:Software]]
[[Category:DOCK]]
[[Category:DOCK 3.6]]

Revision as of 21:51, 13 February 2014

DOCK 3.6 was the primary version of DOCK used in the [Shoichet Lab]] between 1998 and 2013. It was also called DOCK 3.5.54 or even DOCK 3.5.5.4 or DOCK 3.5ens. It has been largely superseded by DOCK 3.7. All docking papers from the Shoichet Lab during that time used this program. It was also used by DOCK Blaster from 2007 until present. We intend to switch over to DOCK 3.7 during 2014.

DOCK 3.5.54 was superseded by DOCK 3.6 in May 2010. DOCK 3.5.54 is no longer available.

List of publications using DOCK 3.5.54

Release Date

DOCK 3.6 was released on April 31, 2010.

Contributors

  • Michael Mysinger - innovations in the calculation of ligand desolvation, as described in Mysinger MM, Shoichet BK, Rapid context-dependent ligand desolvation in molecular docking, J Chem Inf Model. 2010 Sep 27;50(9):1561-73
  • Michael Carchia - code optimizations
  • Ryan Coleman - internal code cleanup (see below)
  • Niu Huang & lab - ligand clustering code (see below)
  • Ryan Coleman & Kim Sharp - Qnifft DOCK 3.6 conversion replacement for delphi

Ligand Desolvation

  • Improved calculation of ligand desolvation, as described in Mysinger MM, Shoichet BK, Rapid context-dependent ligand desolvation in molecular docking, J Chem Inf Model. 2010 Sep 27;50(9):1561-73

Optimizations

  • Speed up of 300 to 500% depending on platform and case by Michael Carchia.
  • First version of DOCK 3 series to use 64-bit and 32-bit versions

Clean up

  • Fast out-of-bound checking, by Ryan Coleman
  • Internal clash checking inside DOCK, by Ryan Coleman

Ligand Clustering

  • Replacement for Single Mode
  • Contributed by Niu Huang's lab.
  • See Dock Ligand Clustering page for more information

Qnifft