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nrbennet / dl_binder_design

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Any reason why cysteine is ommitted by default in ProteinMPNN? Or is that just an accident? #55

Closed ackbar03 closed 9 months ago

ackbar03 commented 9 months ago

Hi,

I noticed the AA Cysteine is omitted by default in the ProteinMPNN design in dl_interface_design.py

parser.add_argument( "-omit_AAs", type=str, default='CX', help='A string of all residue types (one letter case-insensitive) that you would not like to use for design. Letters not corresponding to residue types will be ignored (default: CX)' )

https://github.com/nrbennet/dl_binder_design/blob/bfab591db9a70c9c4eaf449c30ce4a1edcb7c989/mpnn_fr/dl_interface_design.py#L64C1-L64C58

Was this left there by accident or is there a reason for this?

Thanks

nrbennet commented 9 months ago

Cysteines can yield poorly behaved proteins in some systems so we exclude it by default. Feel free to enable them in your design runs!