Category:Docking: Difference between revisions

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'''Molecular docking''' is the process of posing, scoring and ranking small molecules in the binding sites of proteins.  Typically, a large database of molecules such as [[ZINC]] is screened and ranked using a docking program such as [[DOCK]].  The top scoring compounds are reviewed in a [[hit picking party]] and then [[purchased]] and [[tested experimentally]].  There are many good [[molecular docking programs]].  [[Portal:DOCK | DOCK]] is the implementation of molecular docking and virtual screening that we develop and use at [[UCSF]] and [[University of Toronto]].
We use '''Molecular docking''' to screen large libraries of commercially available molecules to prioritize them for purchase or synthesis.


In our lab, a large database of small molecules such as [[ZINC]] is screened using a docking program such as [[DOCK]]. Many other libraries and docking programs are available (below).  The top-scoring compounds are reviewed in a [[hit picking party]] and then purchased and tested experimentally. 


The difference between the Docking category and the DOCK category is that DOCK is specific to our software, whereas Docking includes all docking programs and the approach in general.  
* '''Our current version of DOCK is [[DOCK 3.8]]'''.
* There is a second, independent version of DOCK [[DOCK 6.9]].


[[Category:Jargon]]
{{TOCright}}
[[Category:Portal]]
 
== Docking Programs ==
There are many docking programs. All of them have been successfully used for ligand discovery.  The first three are from UCSF.
* [[DOCK 3]] - latest version is [[DOCK 3.8]] - this is the version our group uses routinely.
* [[DOCK 6]] - latest version is [[DOCK 6.9]]
* [[DOCK 4]]
* [http://www.schrodinger.com Glide]
* [http://www.jainlab.org/ Surflex Dock]
* [http://www.biosolveit.de FlexX]
* [http://www.ccdc.cam.ac.uk GOLD]
* [http://www.molsolft.com ICM]
* [http://www.eyesopen.com FRED]
* [http://www.chemcomp.com MOE]
* [http://autodock.scripps.edu/ AutoDock]
If we have forgotten your program, please add it here.
 
The difference between the Docking category and the [[:Category:DOCK]] category is that DOCK is specific to our software, whereas Docking (this page) includes all docking programs and the approach in general.
[[Category:Software]]
[[Category:Topic]]
[[Category:Topic]]
[[Category:Organization]]

Latest revision as of 18:20, 3 May 2021

We use Molecular docking to screen large libraries of commercially available molecules to prioritize them for purchase or synthesis.

In our lab, a large database of small molecules such as ZINC is screened using a docking program such as DOCK. Many other libraries and docking programs are available (below). The top-scoring compounds are reviewed in a hit picking party and then purchased and tested experimentally.

  • Our current version of DOCK is DOCK 3.8.
  • There is a second, independent version of DOCK DOCK 6.9.

Docking Programs

There are many docking programs. All of them have been successfully used for ligand discovery. The first three are from UCSF.

If we have forgotten your program, please add it here.

The difference between the Docking category and the Category:DOCK category is that DOCK is specific to our software, whereas Docking (this page) includes all docking programs and the approach in general.

Subcategories

This category has the following 3 subcategories, out of 3 total.

D

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