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dauparas / ProteinMPNN

Code for the ProteinMPNN paper
MIT License
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Any way to specify per-residue AA makeups? #23

Closed jadolfbr closed 1 year ago

jadolfbr commented 1 year ago

Sort of like the omit_AAs dictionary, except for individual positions?

dauparas commented 1 year ago

yes, check this flag:

argparser.add_argument("--omit_AA_jsonl", type=str, default='', help="Path to a dictionary which specifies which amino acids need to be omited from design at specific chain indices")

e.g. how to make the input: https://github.com/dauparas/ProteinMPNN/blob/main/helper_scripts/other_tools/make_omit_AA.py

jadolfbr commented 1 year ago

Awesome! Super helpful! Thank you! Would this also work to force specific positions to be a specific residue? I’ve currently been doing that in PyRosetta and then passing it along, but I guess if you use this and set AA weights to 0 vs 1, that could essentially do the trick?

On Mon, Oct 17, 2022 at 12:03 AM Justas Dauparas @.***> wrote:

yes, check this flag:

argparser.add_argument("--omit_AA_jsonl", type=str, default='', help="Path to a dictionary which specifies which amino acids need to be omited from design at specific chain indices")

e.g. how to make the input: https://github.com/dauparas/ProteinMPNN/blob/main/helper_scripts/other_tools/make_omit_AA.py

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dauparas commented 1 year ago

Yes, this should work!