ADL: Query regarding autodock

Diogo Martins diogo.stmart at gmail.com
Tue Apr 14 09:21:13 PDT 2020


Hello,

The success rate for re-docking small molecules is between 60 and 90% (see
https://www.ncbi.nlm.nih.gov/pubmed/29989806). It doesn't always work.
Furthermore, it may be necessary to include explicit waters and/or fix the
protonation state of the ligand and the receptor.

Best,

On Tue, 14 Apr 2020 at 06:47, Chhaya Singh 1820204 <csingh at iiserb.ac.in>
wrote:

> Dear Sir/Madam,
>
> I am trying to perform a docking experiment. I have a query regarding that.
> Is it possible to take a crystal structure of a protein-ligand complex and
> then remove the ligand and dock in the same protein and get the exact pose?
>
> If yes, then I would like to tell that I have tried the above-mentioned
> docking experiment using a crystal structure. But I am not able to get the
> exact pose after docking using autodock tools.
>
> Please help regarding this.
>
> If any queries please let me know.
>
> Regards,
> Chhaya
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