RosettaCommons / RosettaCommons/foundry
Low scoring
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- Dominant language
- Python
- Stars
- 966
- Forks
- 181
- Avg merge
- 4d 4h
- Merged PRs (30d)
- 2
Description
Hello,
I have generated a Slurm pipeline using the CLI based on the Colab example to design 1000 novel proteins (80-140aa) for PPI using RFD3, followed by MPNN and RF3. The issue is that during MPNN, the RFD3 genereated sequence is concatenated with the target sequence as a single polymer and used as input to the RF validation, which overall results in a score below 0.2. The concatenated sequence produces a different 3D structural output, compared to the output of RFD3.
Is this a known bug, or is there a workaround?
Best,
Ronald
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 with the Slurm pipeline generated from the Colab example and trace how the RFD3-generated sequence is passed through MPNN and into RF validation. Compare the sequence and structural inputs at each stage to determine whether concatenation is intended. Done means identifying the cause of the low score and documenting a confirmed fix or workaround.
Written by the indexing model from the issue text.
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