Protein Mutation Scoring

Some scoring functions for predicting the effects of mutations on protein sequences using ESM-2.

Usage

Below are examples on how to run different scoring methods on the mutations.csv file. Valid models are:

• facebook/esm2_t6_8M_UR50D,
• facebook/esm2_t12_35M_UR50D,
• facebook/esm2_t30_150M_UR50D,
• facebook/esm2_t33_650M_UR50D.

You can change the protein sequence to a sequence of your choice, just be sure to update the mutations.csv file to mutations that make sense for your protein. The script zero-indexes the residues by default. So the if you mutate the first residue, this is the $0^{th}$ residue. Adjust the output.csv to whatever name you want for the file you want the output scores to be in. Example usage (masked marginals):

python3 scoring_esm2.py \
  --model "facebook/esm2_t12_35M_UR50D" \
  --sequence "MKTIIALSYIFCLVFA" \
  --dms-input mutations.csv \
  --dms-output output.csv \
  --mutation-col mutant \
  --scoring-strategy masked-marginals 

Example usage (wild-type marginals):

python3 scoring_esm2.py \
  --model "facebook/esm2_t12_35M_UR50D" \
  --sequence "MKTIIALSYIFCLVFA" \
  --dms-input mutations.csv \
  --dms-output output.csv \
  --mutation-col mutant \
  --scoring-strategy wt-marginals 

Example usage (pseudo-perplexity):

python3 scoring_esm2.py \
  --model "facebook/esm2_t12_35M_UR50D" \
  --sequence "MKTIIALSYIFCLVFA" \
  --dms-input mutations.csv \
  --dms-output output.csv \
  --mutation-col mutant \
  --scoring-strategy pseudo-ppl