Re: [AMBER] Docking proteins to DNA

From: Cianna Calia via AMBER <amber.ambermd.org>
Date: Thu, 13 Jun 2024 08:29:19 -0700

In addition to standard docking tools like HADDOCK, you may want to check
out some fairly new tools: AlphaFold 3 and RoseTTAFold-All-Atom.

https://blog.google/technology/ai/google-deepmind-isomorphic-alphafold-3-ai-model/
https://www.science.org/doi/10.1126/science.adl2528

Best of luck,
Cianna

On Wed, Jun 12, 2024 at 1:27 PM James Kress via AMBER <amber.ambermd.org>
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?
>
> There is a plethora of apps one can find mentioned doing a web search.
> What
> would the AMBER community suggest is a best choice?
>
> Thanks for any responses.
>
> Jim Kress
> James Kress Ph.D., President
> The KressWorksR Institute
> An IRS Approved 501 (c)(3) Charitable, Nonprofit Corporation
> "ENGINEERING THE CURE" C
> (248) 573-5499
>
> Learn More and Donate At:
> Website:
> https://urldefense.com/v3/__http://www.kressworks.org__;!!Mih3wA!Gy0xPitwOT9nE1A3k1R3eIr-B1nCSdTiQMDlWEJSrW1l9NFbzFqsM4R6-WLgpNdUFpLUQbhuu3dNbg$
>
> Confidentiality Notice | This e-mail message, including any attachments, is
> for the sole use of the intended recipient(s) and may contain confidential
> or proprietary information. Any unauthorized review, use, disclosure or
> distribution is prohibited. If you are not the intended recipient,
> immediately contact the sender by reply e-mail and destroy all copies of
> the
> original message.
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
>
> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!Mih3wA!Gy0xPitwOT9nE1A3k1R3eIr-B1nCSdTiQMDlWEJSrW1l9NFbzFqsM4R6-WLgpNdUFpLUQbhjb2JDag$
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 13 2024 - 08:30:02 PDT
Custom Search