RosettaCommons / RosettaCommons/RFdiffusion
partial diffusion with an antibody-antigen complex structure
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- Dominant language
- Python
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Description
I have an antigen-antibody complex structure, and I performed diffusion on part of the antibody sequence. The current parameters are as follows, but the result connects the two chains of the antibody together. How should I modify the parameters?
run_inference.py inference.output_prefix=rfd_diffuser20/test inference.input_pdb=test.pdb 'contigmap.contigs=["228-228/0 C229-503"]' diffuser.partial_T=20 inference.num_designs=1000 'contigmap.provide_seq=[0-29,31-227]' 'ppi.hotspot_res=[C262,C263,C265,C266,C267,C268,C269,C270,C315,C316,C317,C319,C321,C329,C344,C345,C346,C348,C374,C375,C376,C377,C393,C395,C397,C399,C434,C435,C436,C437,C438,C451,C455,C457,C458,C459,C460,C462,C465,C467,C469]'
Contributor guide
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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 run_inference.py and reproduce the supplied command using test.pdb. Read the contigmap, provide_seq, ppi.hotspot_res, and diffuser.partial_T configuration documentation or entry points, then inspect how the antibody chains are represented and connected. Done means identifying a parameter configuration that preserves the intended chain separation and documenting the reproducible command.
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
- Mostly clear
- Newbie friendliness
- 30/100