This repository contains a discriminator guided approach for functional protein inverse folding

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To set up a new conda environment with required packages,

conda create -n inverse python=3.9
conda activate inverse
conda install pytorch cudatoolkit=11.3 -c pytorch
conda install pyg -c pyg -c conda-forge
conda install pip
conda install pandas biopython
pip install biotite
pip install git+https://github.com/facebookresearch/esm.git

Quickstart

To sample sequences for a given structure in PDB or mmCIF format, use the sample_sequences.py script. The input file can have either .pdb or .cif as suffix.

For example, to sample 3 sequence designs for the golgi casein kinase structure (PDB 5YH2; PDB Molecule of the Month from January 2022), we can run the following command from the examples/inverse_folding directory:

• The "--loss_type" should be chosen among ['Solubility', 'Stability', 'Both']

python sample_sequences.py \
    --pdbfile data/5YH2.pdb \
    --chain C --temperature 1 --num-samples 3 \
    --outpath output/sampled_sequences.fasta \
    --loss_type Solubility \
    --stepsize 0.1 \
    --num_iterations 2 \
    --kl_scale 0.5