[Dock-fans] DOCK for an enzyme with cofactor

John Irwin jji at cgl.ucsf.edu
Wed Oct 12 05:55:56 PDT 2005

Hi Ying

I've had some success docking to metalloenzymes. The work appeared recently:
Irwin, Raushel and Shoichet, Biochemistry 2005, 44, 12316-12328. As to
whether docking can be done with high accuracy: docking to any target, with
a metal or without, can be challenging. Metals and co-factors exacerbate the
problems latent in the docking calculation, so you have to be even more
careful than with a "plain vanilla" target.

We like controls. First convince yourself that the docking calculation can
reproduce experimentally observed geometries (or, in the absence of a
crystal structure, with structures that are consistent with experimental
data). Then, you'll need to convince yourself that the docking calculation
scores known binders among the top of some database of decoys.

Good luck with docking!


> -----Original Message-----
> From: dock-fans-bounces at docking.org 
> [mailto:dock-fans-bounces at docking.org] On Behalf Of ying xiong
> Sent: Sunday, October 09, 2005 1:00 AM
> To: dock-fans at docking.org
> Subject: [Dock-fans] DOCK for an enzyme with cofactor 
> Dear sir,
>      I want to use DOCK to do docking calculation for a 
> protein and ligands. The active site of this protein includes 
> cofactor and metal ion, so they are important and can not be 
> ignored. I wonder whether DOCK program can calculate the 
> energy score of this protein and ligands with high accuracy.
>         ying xiong
>         yxiong99 at 163.com
>           2005-10-09
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