bytedance / bytedance/Protenix
Performance difference after updating to 0.5.0
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Description
I have used v0.2.0 to predict the ligand-protein stcuture of one protein without known struture. It outputed a pTM = 0.67 & ipTM = 0.97. After updating to v0.5.0, using the same json input, it outputs a pTM = 0.16 & ipTM = 0.77.
By manually checking, the predictied strutures by V0.2.0 and V0.5.0 are very inconsistent. Under such condition, should I down-grade protenix to v0.2.0? What is the reason for such difference?
Thanks,
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 reproducing the reported prediction with the same JSON input under v0.2.0 and v0.5.0, then compare the resulting pTM, ipTM, and predicted structures. Determine whether the difference is an intentional version change or a regression, and document the cause and expected behavior.
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Assessment
- Tech stack
- python
- Domain
- bioinformatics, machine-learning
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100