RosettaCommons / RosettaCommons/RFdiffusion
questions for pAE compute
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Description
Hello! I have recently read your article "Atomically accurate de novo design of single-domain antibodies" and am very interested in it. In this article, there is a computational metric called pAE (predicted Aligned Error). In my studies, pAE refers to the alignment error between each pair of residues. If I calculate pAE for a segment of the sequence (for example, the CDR3 region), the result should be in the form of a matrix that stores the pAE between each pair of residues. How do you integrate the pAE of each pair of residues into a single value? And how is the criterion of pAE being less than 10 derived?
If you can clarify my doubts, I would be very grateful!
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Research direction
Start with the cited article and the issue's description of predicted Aligned Error (pAE), then trace how RFdiffusion reports or uses pAE for residue segments. Done means documenting how pairwise pAE values become a single segment value and explaining the origin of the less-than-10 criterion; no repository files or tests are identified in the issue.
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Assessment
- Tech stack
- python
- Domain
- bioinformatics, machine-learning
- Issue type
- Documentation
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100