I also got nice results with pyDockDNA:
https://model3dbio.csic.es/pydockdna
I suggest trying several programs and comparing the results...
Good luck!
Andrea
On Thu, Jun 13, 2024 at 11:28 PM James Kress via AMBER <amber.ambermd.org>
wrote:
> Thank you David.
>
> -----Original Message-----
> From: David A Case <dacase1.gmail.com>
> Sent: Thursday, June 13, 2024 10:15 AM
> To: jimkress_58.kressworks.org; AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Docking proteins to DNA
>
> On Wed, Jun 12, 2024, James Kress via AMBER wrote:
>
> >I am looking to find suggestions on the best application for docking
> >proteins to DNA.
> >
> >Is AMBER alone sufficient or are other apps like npDOCK, HAADOCK, HDOCK
> >better suited to this task?
>
> Other apps are definitely needed: Amber is not designed to do docking. I
> hope you will get some suggestions that concentrate on protein--DNA
> docking.
> Be sure to look for application papers in this area, and see what was used.
>
> ....dac
>
>
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Received on Fri Jun 14 2024 - 02:00:02 PDT
