RosettaCommons / RosettaCommons/RFdiffusion
Possible to specify secondary structure for specific part of a diffused protein without using fold conditioning on defined scaffolds
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- Dominant language
- Python
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Description
I would like to use RFdiffusion to design an alpha-helical linker between one protein and another protein. Is there a way to specify that a certain part of a design should be alpha-helical without fold conditioning on a specific protein scaffold? My current thought is to use motif scaffolding with the following contig:
'contigmap.contigs=[A1-100/70-150/B1-100/70-150/A101-200]'
Where chain A is the first protein I want to link and chain B is the second. Here, the link to chain B is being inserted in place of a loop in chain A (i.e. primary structure will be ProteinA(first half)-alphaHelicalLinker-ProteinB-alphaHelicalLinker-ProteinA(second half).
I currently cannot see a way to specify that the linker ('contigmap.contigs=[A1-100/70-150/B1-100/70-150/A101-200]') must be alpha helical. Is it possible to do this in an easy way at the command line or do I need to do something janky with a dummy pdb to fold condition on for the linker region?
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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 the motif-scaffolding entry point and the contigmap.contigs command-line option described in the issue, then compare it with fold conditioning. Determine whether linker secondary structure can be specified without a scaffold; done means documenting a supported command-line approach or scoping the required feature.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, machine-learning
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100