RosettaCommons / RosettaCommons/foundry
Using Modelforge -RF3 to test protein folding of sequences containing D-residues in main chain.
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Description
The "Training RF3" section of the prerprint suggests that better handling of chirality with this new framework is possible.
Is it possible to provide a single chain sequence that contains both L and D amino acids to predict folding? For a seqence containing multiple D-residues, would each D-amino acid need to be treated as an individual NCAA that must be specified with a corresponding SMILES, following the format in your NCAA example?
Thank you,
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Research direction
Start by reading the linked preprint's “Training RF3” section and the referenced tests/data/example_with_ncaa.json example. Determine whether mixed L- and D-residue single-chain sequences are supported and whether each D-residue requires an NCAA SMILES definition. Done means documenting the supported input format and any required changes or limitations.
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Assessment
- Tech stack
- python
- Domain
- machine-learning
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100