sokrypton / sokrypton/ColabFold
Can I use PDB70 instead of PDB100?
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Description
Current Behavior
Hi,
I have been running ColabFold v1.5.2-patch to predict a protein complex. I have noticed that the predicted structure I was getting with the previous PDB70 database is much better than the one I am getting with the current PDB100 database. Is there a way to run this prediction with PDB70 now? Or could this change be due to some parameter change? I have been using the default settings. I have already tried both complete and greedy pairing.
Context
I have some new analyses to do and I would like to do it in the same way as I did before ( before the database got updated to pdb100) which gave me a better prediction.
Your Environment
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- Git commit used
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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
No file, test, or entry point is named. Start by reviewing how ColabFold v1.5.2-patch selects PDB70 or PDB100 under the default settings, then compare the complete and greedy pairing paths. Done means establishing whether PDB70 remains selectable and whether the database update changed another parameter.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics, databases
- Issue type
- Bug
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100