[Dock-fans] metal-containing ligand

John J. Irwin jji at cgl.ucsf.edu
Mon May 7 10:18:42 PDT 2007


Hi Agnes

Sorry, I didn't read your note carefully. (I have Monday Attention
Deficit Disorder).

We have no experience docking metal containing ligands. The odds are
certainly stacked against you, since most of the programs to prepare
ligands are in general not parameterized for metals. Moreover, most
docking scoring functions do not work well with metals, in my experience.

Good luck.

John

John J. Irwin wrote:
> Hi Agnes
>
> You might like to look at our paper: Irwin JJ, Raushel FM, Shoichet BK,
> "Virtual screening against metalloenzymes for inhibitors and
> substrates.", Biochemistry, 2005, 44(37),12316-28. DOI
> <http://dx.doi.org/10.1021/bi050801k>.
>
> With Au, you may well have electronic effects that make the energetics
> too subtle to be captured by classical mechanics approaches.
>
> Good luck!
>
> John
>
>
> Simon Ágnes wrote:
>   
>> Dear Dockers,
>>
>>  
>>
>> I am wondering, if anyone has experience in docking metal-containing
>> ligands, (by using any docking programs).
>>
>>  
>>
>> In fact, my ligand contains gold  ( Au(I) ),  - so I would be greatful
>> to hear of any docking program that could reliably treat my ligand.
>>
>>  
>>
>> Regards,
>>
>>  
>>
>> Agnes      
>>
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>>
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