Hi Xiaokun,

  The ChimeraX team has talked about RFDiffusion but I don't think anyone has read the paper or tried it yet.  In general ChimeraX is good for fast computations (seconds or minutes).  If RFDiffusion takes hours I'm not sure how much sense it would make to run it from ChimeraX.  Maybe if the ChimeraX were good for specifying the constraints as input to RFDiffusion it might make sense.  Another difficulty is that if it needs to run on the cloud because it requires high-end graphics or databases then we don't have the computer resources to offer that.  For AlphaFold and ESMFold ChimeraX runs predictions on Google Colab.

  We'll have to investigate RFDiffusion further to see if ChimeraX can offer a useful interface.

Tom


On Jul 22, 2023, at 7:13 PM, Tom Ferrin via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:



Sent from my iPhone

Begin forwarded message:

From: "Shu, Xiaokun" <Xiaokun.Shu@ucsf.edu>
Date: July 22, 2023 at 9:41:52 AM AKDT
To: "Ferrin, Thomas" <tef@cgl.ucsf.edu>
Subject: RFdiffusion in ChimeraX?

Hi Tom, 
Are you thinking of incorporating a protein de novo design e.g. RFdiffusion into ChimeraX? The AlphaFold is very useful in predicting structure and PPIs. Thanks a lot!

Best,
Xiaokun
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Xiaokun Shu, Ph.D (he/him/his)
Professor, Department of Pharmaceutical Chemistry
Investigator, Cardiovascular Research Institute
Member, Hellen Diller Family Comprehensive Cancer Center
University of California, San Francisco
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
555 Mission Bay Blvd South
Smith Cardiovascular Research Building, Room 452Y
PO Box 589001, MC Box 3122
San Francisco, CA 94158-9001
Tel:  +1 (415) 617-5675
================================






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