[chimerax-users] unifold

[Roger Leng]

Many thanks, Tom.
I watched your lots of "youtube". It is great to learn and use ChimeraX. I
tried unifold.ipynb (online), but, un-luck, failed several times with paid
program. Interestingly, I failed several times to use alphafold2.ipynb
(online); but I used ChimeraX with Alphafold successfully for complex
prediction.
In addition, I was told that RoseTTAFold (Linux) could use for complex
prediction. I am installing RoseTTAFold in Linux. Again, I filed several
times to use RoseTTAFold.ipynb (online). Actually, I do not understand why
I always filed to use AlphaFold or RoseTTAFold online (.ipynb with the paid
program, Pro+).
Thank you again.
Have a great day!
Roger
Roger Leng,
Faculty of Medicine,
University of Alberta,
Canada

On Wed, Apr 12, 2023 at 4:05 PM Tom Goddard <goddard at sonic.net> wrote:

> Hi Roger,
>
>   Unifold looks interesting.
>
> https://github.com/dptech-corp/Uni-Fold
>
> It is an open source reimplementation of AlphaFold using the PyTorch
> machine learning framework done by a China-based company called DPTech (
> https://www.dptech.com/).  From reading the github page it sounds like
> one of its main advantages over AlphaFold is that the training code and
> protocol is all open source.  Code for the training of AlphaFold was never
> made available as far as I know.
>
>   That is all nice, but what are the best reasons for our UCSF lab to try
> to offer this in ChimeraX?  The ChimeraX AlphaFold user interface took
> about 2 months of development with ongoing maintenance.  I'd estimate the
> cost so far at $30,000.  ChimeraX is funded by NIH grants.  Is it worth
> expending similar resources to implement and maintain an interface to
> UniFold?
>
> Tom
>
>
> On Apr 12, 2023, at 2:24 PM, Roger Leng via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
>
> Dear Administrators,
>
> Is it possible to add "unifold" in your prediction, just like Alphafold?
>
> Thank you.
>
> Sincerely,
>
> Roger Leng
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