Chai prediction with ligands
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Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 35/100
- Issue type
- Bug
- Clarity
- Mostly clear
- Activity status
- Stale
- Tech stack
- python
- Domain
- machine-learning
Research direction
Trace the Chai1 pipeline that generates input FASTA files and the RFdiffusion2 output backbone residue numbering. Reproduce a run with two ligands sharing a name, then verify that ligands are not written as protein entries and that both ligand copies remain in the Chai1 input and metrics results.
Written by the indexing model from the issue text.
Description
Hi!
I've noticed two bugs relating to Chai1 prediction of ligands when running the pipeline.
- Ligands are incorrectly added as 'protein' entries into the Chai1 input fasta files.
- If backbones are generated around two ligands of the same name, then they will both be incorrectly given the same residue number in the RFdiffusion2 output backbone. This doesn't affect the LigandMPNN step, but it means that only one copy of the ligand is added to the Chai1 input fasta file. This means the predicted structures only have one of two ligands, throwing off the metrics step.
Happy to share more info if needed. Thanks!
- Dominant language
- Python
- Stars
- 443
- Forks
- 70
- PR merge metrics
- No merged PRs in 30d
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