google-deepmind / google-deepmind/alphafold
Alphafold subsampling "max_msa_clusters"
- Dominant language
- Python
- Stars
- 14.9k
- Forks
- 2.9k
- PR merge metrics
- No merged PRs in 30d
Description
There have been several [recent studies](https://www.biorxiv.org/content/biorxiv/early/2023/07/27/2023.07.25.550545.1.full.pdf) showing how decreasing the amount of MSA cluster centers, in tandem with the number of "extra sequences" used can increased volatility in predictions to sample more possible conformations. The options to change the number of MSA cluster centers and extra sequences have been added to Colabfold, but I am wondering which variables and scripts I need to change in my local install to change the number of cluster centers. As of now I have changed the "max_msa_clusters" variable in /model/config.py, but I am not sure if this change is propagating. Can anyone confirm how to get this option locally? Thank you in advance.
Contributor guide
Assessment
This issue has not been assessed yet.