ADL: Autodock vs. Dock6

Rudy J. Richardson rjrich at umich.edu
Thu Sep 23 13:07:22 PDT 2010


YJ:

Ultimately, the choice of a docking program depends upon how well it can 
predict ligand-protein poses for your particular application. You can get 
some idea of how well autodock compares to some other programs for 
particular receptors and sets of ligands through recent publications. In 
addition, you could carry out your own comparisons.

As you have observed, one advantage of autodock is that it is widely used 
and results from the program are frequently published. Like DOCK, autodock 
is undergoing continuing improvement by its developers. Unlike DOCK, which 
runs only in a unix environment, autodock is available for all popular OS 
platforms (linux, Mac OSX/unix, and Windows), and it has been incorporated 
into other software packages as the docking "engine" (e.g., 
YASARA-Structure). This gives autodock advantages with respect to 
flexibility and ease of use.

My impression is that overall, top commercial docking programs such as 
GLIDE (Schrodinger) and GOLD (CCDC/Accelrys) might perform somewhat better 
than autodock, but autodock fares quite well among software that is free 
for academic users.

Best regards,

Rudy Richardson
University of Michigan

On Thu, 23 Sep 2010, korea0914 wrote:

>
> Hi, I'm just getting familiar with the world of computational docking.
>
> I started as a DOCK6 user. However, autodock is the most frequently used
> programs in many publications.
>
> Is autodock superior to dock6?
>
> What are some of its advantages and disadvantages?
>
> Thank you.
>
> YJ
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