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ProDESIGN-LE

ProDESIGN-LE, which is an accurate and efficient protein sequence design approach, designs a sequence using a transformer to iteratively maximize the overall fitness between residues and their local environments.

ProDESIGN-LE's corresponding article, Accurate and efficient protein sequence design through learning concise local environment of residues, is currently published.

Basic Usage:

python3 design.py best.pkl 0008.pdb -o . -c . -d cuda:0

python3 design.py best.pkl <PDB dir> [-o output_path] [-c cache_path] [-d device] [-n number_designed_seqeunce]

Options

Fix specific residues during design. Add the flag --constrain <constrain.txt>, where constrain.txt is a file structured as follows:

1 A
2 R
3 N

The first column represents the 1-indexed index of the residue, while the second column represents the one-letter residue symbol. Add as many rows as you like.

Requirements:

1. pytorch
2. einops
3. biopython