search

uw-ipd / RoseTTAFold2NA

RoseTTAFold2 protein/nucleic acid complex prediction
MIT License
310 stars 69 forks source link

RoseTTAFold2NA Google Colab #41

Open AAVwhit opened 1 year ago

AAVwhit commented 1 year ago

Is there a google colab for this program like the one available for RoseTTAFold?

sirius777coder commented 9 months ago

Also have this problem

gezmi commented 8 months ago

+1 for this feature!

mackevinbraza commented 7 months ago

This will definitely an excellent feature! +1

denizkavi commented 7 months ago

I made a simple interface to RoseTTAFold2NA, it can be accessed here: https://www.tamarind.bio/app. Should work the same as a Colab Notebook would have. (No affiliation with the authors of RoseTTAFold2NA)

image
ExactMoose commented 7 months ago

I believe the problem lies in the backend of how Google Colab works. In order to implement this on a Colab notebook, you would need enough disk space to actually store the databases, which even a Colab Pro+ instance with A100 GPU + High RAM only has about 200 GB of actual disk space; therefore, setting this up would likely require an external web server. The most storage-heavy part of the script is the MSA, and for example, the AlphaFold2 Colab Notebook, which everyone uses, uses the Mmseqs2 web server to perform the MSA (i.e. the alignment database is not stored on the colab notebook itself.)