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 to prioritize compounds for aquisition and experimental testing.  Typically, a large database of small molecules such as [[ZINC]] is screened 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 molecular docking programs to choose from (see below).  [[DOCK 3]] is the implementation of molecular docking and virtual screening that we develop and use at [[UCSF]].
We use '''Molecular docking''' to screen large libraries of commercially available molecules to prioritize them for purchase or synthesis.


The goal of molecular docking screens is often ligand discovery - new chemical matter than can be optimized using medicinal chemistry techniques.  Another approach to ligand discovery is to simply use [[cheminformatics]] methods such as [[ZINC]] to identify purchasable compounds.
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]].


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== Docking Programs ==  
== Docking Programs ==  
There are many docking programs. All of them have been successfully used for ligand discovery.  The first three are from UCSF.  
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 3.7]] - this is the version our group uses routinely.
* [[DOCK 3]] - latest version is [[DOCK 3.8]] - this is the version our group uses routinely.
* [[DOCK 6]] - latest version is [[DOCK 6.7]]
* [[DOCK 6]] - latest version is [[DOCK 6.9]]
* [[DOCK 4]]
* [[DOCK 4]]
* [http://www.schrodinger.com Glide]
* [http://www.schrodinger.com Glide]

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.

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