alphafold2mmopt

Based on alphafold2, alphafoldmmopt is developed to optimize molecules from any protein-generation model.

dependence

conda install openmm
pip install dm-tree
pip install biopython
pip install dm-haiku
conda install -c omnia pdbfixer
pip install pytorch

installation and run

• install

pip install alphafold2mmopt

• running: for a given any *.pdb file

# shell
alphafold2mmopt *.pdb

# python
from proteinopt.common.protein import Protein
from proteinopt.relax.localminimizer import relax
prot = Protein(pdbname)
opt_pdb=relax(prot)

Updation

v0.2

1. Use pytorch instead of Jax to accelerate lDDT matrix calculation.

The lDDT calculation time can be reduced from 3s to 0.1s.

2. Reconstruct api for Protein object and reduce repeated clean operation.