Comments (4)
BaozCWJ
commented on September 26, 2024
I think that some database of ColabFold can be used by Uni-Fold with some annual settings of database path.
Also, you can try Uni-Fold Colab, which can use the same pipeline as ColabFold for searching MSA and template. If you want to run Uni-Fold with ColabFold's MSA file in your local device, maybe you need some effort to rewrite some code from the notebook. Hope it helpful for you.
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tubiana
commented on September 26, 2024
Hi :)
Thank you for your reply :)
I would like to model an oligomer of 12 protein of 500(ish) residues, unfortunatly Google Colab is not enouth powerfull for that..
But I know you are working on a symmetry version of unifold (which is exactly what I need =D), so I might just wait for that :)
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ZiyaoLi
commented on September 26, 2024
Hi @tubiana we put this (predict directly with a3m) on our todo list and are working on it.
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FranceCosta
commented on September 26, 2024
Hi @ZiyaoLi. Is there any updates on predicting directly from .a3m?
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Related Issues (20)
- Missing import in Colab HOT 1
- colab error HOT 8
- Is total_step fixed? HOT 2
- import_jax_weights_ failed on AlphaFold-Multimer 2.3.0 HOT 3
- parameters are missing in the pretrained weights HOT 4
- Multi node training HOT 3
- Could not find path to the "hhblits" binary
- Run Uni-Fold with Bohrium Apps
- FileNotFoundError: No such file or directory: '/C.feature.pkl.gz' HOT 1
- questions on installing on Ubuntu Linux 22.04 HOT 1
- recreating homo_search.py output -- minimal version HOT 3
- competition multimer analysis -- does chain order matter? HOT 7
- model name for all alphafold parameters HOT 1
- multi-gpu inference
- convert_unifold_to_alphafold.py?
- UniFold crash: unable to find SCOPdata (a bug that has popped up in ColabFold, & there is a straightforward reason and patch) HOT 2
- Training with linkers
- Symmetry code doesn’t work HOT 4
- Unifold-Musse training and finetuning scripts as well as the ability to use PDB templates
- Unifold on custom a3m MSA files
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