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...> 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@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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users