DOCK 3.6

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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 It has been largely superseded by DOCK 3.7.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DOCK 3.5.54 was superseded by DOCK 3.6 in May 2010.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.

Techniques

  • Magdalena will put the link to how to do multiple conformations right here. thank you.

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

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