RosettaCommons / RosettaCommons/foundry
issue with mpnn and RF3
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- Dominant language
- Python
- Stars
- 966
- Forks
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- Avg merge
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- Merged PRs (30d)
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Description
My purpose is to design a protein binder. I ran mpnn on RFD3 generaed backbones, the fasta file from mpnn contains concatenated sequence (Target sequence + Binder sequence). Is this the format of fasta file that i should be getting from mpnn.? Also for running RF3 i made json file from fasta in which extracted A,B and C chains were present. The ranking scores that i got after RF3 were poor. I can't understand where i might be lacking. So can you verify? Also i'm running all the commands through CLI.
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 reviewing the MPNN FASTA output and the RF3 JSON conversion described in the issue, including how chains A, B, and C were extracted. Reproduce the CLI workflow and compare the generated formats with the expected inputs. Done means identifying whether the concatenated sequence or chain conversion explains the poor RF3 ranking scores.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, cli, machine-learning
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100