RosettaCommons / RosettaCommons/RFdiffusion
The cyclic peptides generated by RFdiffusion are not closed.
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- Python
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Description
I can't obtain the correct cyclic peptide backbone pdbs, when I use the RFdiffusion pipeline.
All the cyclic peptides generated by RFdiffusion are not closed at their C-terminus and N-terminus, which just have a cyclic conformation. I use the standard pipeline provided by RFdiffusion authority. Show you below:
python /HOME/scz0bp0/run/zzy/RFdiffusion/scripts/run_inference.py
--config-name base
inference.output_prefix=/HOME/scz0bp0/run/zzy/output/RFdiffusion_output/xxx
inference.num_designs=10
'contigmap.contigs=[10 A18-132/0]'
inference.input_pdb=/HOME/scz0bp0/run/zzy/input/xxx.pdb
inference.cyclic=True
diffuser.T=50
inference.cyc_chains='a'
ppi.hotspot_res=['A56','A58','A113','A115','A121','A123'] \
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Research direction
Reproduce the reported command through scripts/run_inference.py with inference.cyclic=True and inference.cyc_chains='a'. Inspect the cyclic-peptide handling reached by that entry point and compare the generated PDB termini. Done means the generated backbone has the intended closed C- and N-terminus connection.
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
- 35/100