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.
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]
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.
- pytorch (checkout https://pytorch.org/get-started/locally/ for how to install)
- einops
pip install einops - biopython
pip install biopython