[chimerax-users] AlphaFold database is free, but running new prediction is for noncommercial use

[Elaine Meng]

Hi KDY,
I don't know the answers to some of the questions, but it looks like you might be doing this work for a company (for commercial purposes).

In that case, I thought that I should mention that running an AlphaFold calculation on Google Colab is for noncommercial use only, because of the trained model parameters:
<https://github.com/deepmind/alphafold/#model-parameters-license>

However, getting the already-predicted structures from the AlphaFold database is free for everyone:
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html>

And you can get the AlphaFold code for free on github, but then (if I understand correctly) you would need to train it yourself to get the associated parameters.

As far as I know, Alphafold prediction is for single chain only.  I read that RoseTTaFold predicts complexes of multiple chains,  but I haven't used it.  See for example this article mentioning both programs:
<https://cen.acs.org/analytical-chemistry/structural-biology/Accurate-protein-structure-prediction-AI/99/i26>

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

P.S. also we require licensing ChimeraX for commercial use, please see
<https://www.rbvi.ucsf.edu/chimera/commercial_license.html>

> On Sep 24, 2021, at 1:11 AM, dongyoung kim via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi. I'm researching protein 3D structure to develop the new drug.
> 
> In recent, I'm using the Alphafold function in Chimera X daily version.
> 
> I have 4 questions.
> 
> First, if I use Alphafold to predict my important project data, is it keep secure privately?
> I want to keep my data secret. It shouldn't be open to anybody without me. 
> 
> Second, when I using Alphafold in ChimeraX, I faced some error messages that mean 'Not enough disk volume. please remove past data.'. I'm not familiar with google colab...how can I manage the disk to remove past data or expand disk volume? 
> 
> Third, how can I improve the speed of alphafold prediction? ChimeraX shows some resources like ram, disk. 
> 
> fourth, I want to operate simultaneously Alphafold prediction to predict 2 or more structures. Is it possible? 
> 
> 
> If there need some pay to improve the second, third, fourth question, please let me know methods.
> Many thanks.
> 
> -from KDY
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