flexs.landscapes.bert_gfp¶

Defines the BertGFPBrightness landscape.

class flexs.landscapes.bert_gfp.BertGFPBrightness[source]¶

Green fluorescent protein (GFP) brightness landscape.

The oracle used in this lanscape is the transformer model from TAPE (https://github.com/songlab-cal/tape).

To create the transformer model used here, run the command:

```tape-train transformer fluorescence –from_pretrained bert-base
–batch_size 128 –gradient_accumulation_steps 10 –data_dir .```

Note that the output of this landscape is not normalized to be between 0 and 1.

gfp_wt_sequence[source]¶

Wild-type sequence for jellyfish green fluorescence protein.

gfp_wt_sequence = 'MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK'[source]