ADL: How to dock mulitple ligands to one receptor/protein

Gustavo Seabra gustavo.seabra at gmail.com
Mon Nov 2 07:41:36 PST 2020


This may be what you are looking for, although I don't know if they have
the code available:

(1) Li, H.; Li, C. Multiple Ligand Simultaneous Docking: Orchestrated
Dancing of Ligands in Binding Sites of Protein. J. Comput. Chem. 2010,
2014-2022.
https://onlinelibrary.wiley.com/doi/10.1002/jcc.21486


--
Gustavo Seabra.


On Fri, Oct 30, 2020 at 10:21 PM Van Dam, Hubertus <hvandam at bnl.gov> wrote:

> Hi Fatahiya,
>
> Autodock only docks one ligand at a time. To dock two ligands
> simultaneously you want to run two instances of Autodock at the same time
> each docking one ligand. To automate doing that within a single node you
> could use something like GNU parallel (see:
> https://www.gnu.org/software/parallel/). Just be careful to make sure
> that you use unique filenames in each docking calculation.
>
> Best wishes,
>
>     Huub
>
>
> -----------------------------------------------------------------------------------------------------
> Hubertus van Dam, 631-344-6020, hvandam at bnl.gov
> Brookhaven National Laboratory
>
>
> On 10/30/20, 20:26, "autodock-bounces at scripps.edu on behalf of fatahiya
> mohamed tap" <autodock-bounces at scripps.edu on behalf of
> fatahiyamohamedtap at gmail.com> wrote:
>
>     Hi,
>
>     May I know how to dock two ligands to one protein at the same time or
>     simultaneously?
>
>     Thank you in advance for your kind help.
>
>     Regards,
>     Fatahiya
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