Subject: Re: CCL:Autodock and Rigid Body Docking

From: Felipe Pineda <pineda[at]imb-jena.de>
Date: Tue, 16 Sep 2003 09:26:33 +0200

hi Chris,

a little bit late, but better than never ;-)

take a look at the following paper by my former boss, Martin Zacharias:

Zacharias, M.Protein-protein docking with a reduced protein model accounting for
side-chainflexibility.Protein Sci  12(2003)1271-82

Maybe you can then contact him directly for more details.

Best regards

Felipe

Dominique Vlieghe schrieb:

> Hi Chris,
>
> In AutoDock, the ligand is made flexible by defining the torsion angles
> that should vary. If you chose 0 torsion angles, your ligand would be
> regarded as being rigid. Furthermore, you can chose whichever torsion
> angle you desire to be kept flexible, as long as you do not have more
> than 32. This means about 8-16 side chains, depending on their size. Of
> course, the target will always be rigid...
>
> Someone else replied to you that ZDock is a good tool to do
> protein-protein docking. I agree with him when the two proteins have
> conformation very similar to the bound conformations. The perfomance
> however drops considerably when you work with homology models. I must
> say that I did not test RDock yet.
>
> (...)

--
Dr. Luis Felipe Pineda De Castro
EnTec GmbH
Structural Bioinformatics and Drug Design
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