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dauparas / ProteinMPNN

Code for the ProteinMPNN paper
MIT License
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What's the numbering scheme for fixed_residues? #63

Closed tony-res closed 12 months ago

tony-res commented 1 year ago 
{"original": {"H": [26,27,28,29,30,35,36,37,38,56,57,58,59,62,63,64,65,105,106,111,112,113,114,115,116,117], "L": [27,28,29,30,36,37,38,56,57,65,105,106,107,108]}}

I'm trying to fix the CDR regions so that they are not changed by ProteinMPNN. However, I don't seem to have the right numbering (see the .jsonl above).

Is the numbering just the actual position in the string? Does it start at 0 or 1? Is it Clothia? Is it Kabat?