sokrypton / sokrypton/ColabFold
AlphaFold2 predictions are less efficient with the latest version
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Description
Expected Behavior
The predictions are worse with the latest version of sokrypton/ColabFold
In the past I used the following link, but it is getting an error now:
https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/beta/AlphaFold2_advanced.ipynb
Currently I'm using the link (merge beta into main):
https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb
Current Behavior
More or less the same prediction between the two sites. In fact, the result with the beta site corresponds to a pdb 6sdz file from Proline 11 to Lys35, which is proof of the effectiveness of the beta version.
Steps to Reproduce (for bugs)
ColabFold Output (for bugs)
File enclosed containing the same prediction on the two sites
Context
Providing context helps us come up with a solution and improve our documentation for the future.
Your Environment
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by comparing the linked beta/AlphaFold2_advanced.ipynb and AlphaFold2.ipynb Colab entry points, then inspect Results.pdf for the reported prediction differences. Reproduce the same input in both notebooks and trace the settings or workflow differences. Done means the regression has a reproducible cause and a documented resolution.
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Assessment
- Tech stack
- jupyter-notebook
- Domain
- bioinformatics, machine-learning
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100