DOCK 3.6: Difference between revisions

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DOCK 3.5.54 is a substantially modified version of DOCK 3.5 used by the Shoichet Lab and available under the normal UCSF DOCK licensing terms (i.e. free to academics). All docking papers that have come out of this lab have used this program.
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 It has been largely superseded by [[DOCK 3.7]].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.


== List of publications using DOCK 3.5.54 ==
DOCK 3.5.54 was superseded by [[DOCK 3.6]] in May 2010. DOCK 3.5.54 is no longer available.
Many are directly cited on the
[http://shoichetlab.compbio.ucsf.edu/publications.php Shoichet Lab Publications Page] and referenced cited therein. It would be great if someone would format them nicely here.


== List of publications of the methods in DOCK 3.5.54 ==
*[[DOCK 3.6 User Manual]]
*[[DOCK 3.6]]
*[[BKS lab Structure preparation]]


* Kuntz, Shoichet 1993, [http://dx.doi.org/asdf/2342324 here]
* Original documentation as [[Image:Dock3 5refman.pdf | PDF ]]
* Shoichet & Lorber papers


* Original documentation ([[Image:Dock3 5refman.pdf | PDF ]])
= List of publications using DOCK 3.5.54 =
== Related websites ==
* [http://shoichetlab.compbio.ucsf.edu/publications.php Shoichet Lab Publications Page]
* [http://shoichetlab.compbio.ucsf.edu Shoichet Lab Website]
* [http://dock.compbio.ucsf.edu Official DOCK website] where DOCK may be requested, free to academics, a bargain for everyone else.


* [[Install DOCK 3.5.54]]
* [[INDOCK_for_DOCK_3.6]]
= 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.
{{TOCright}}
= 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 =
* Replacement for Delphi, still Poisson Boltzmann electrostatics
* Contributed by Kim Sharp & Ryan Coleman
* See  [[Qnifft DOCK 3.6 conversion]] page for more information.
* Please cite http://10.0.3.234/bip.360360210 and http://dx.doi.org/10.1016/S0006-3495(98)77566-6


[[Category:Software]]
[[Category:Software]]
[[Category:DOCK]]
[[Category:DOCK 3.6]]
[[Category:DOCK Blaster]]
[[Category:Freecom]]

Latest revision as of 22:15, 2 January 2019

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