Design your protein for given backbone structure on PyMOL!
Run protein MPNN and predict the structure by ESM API on PyMOL.
Sequence design part was adapted from ProteinMPNN@ColabDesign by @sokrypton and his collaborators.
Structure prediction part was adapted from PymolFold by @JinyuanSun
- colabdesign
- matplotlib (required by colabdesign)
- requests
Install them via pip bundled with your PyMOL. Be careful not to destroy your (purchased) PyMOL.
Installation of colabdesign
pip -q install git+https://github.com/sokrypton/[email protected]
From PyMOL console,
run design.py
Then
design selection, name
For example,
load mybackbone.pdb
design mybackbone, myfirstdesign
will yield the designed model templated by your backbone and named myfirstdesign.
This is a repository under development. Issues and PR would be welcomed.
Add reference for ColabDesign and proteinMPNN here
@article{lin2022language,
title={Language models of protein sequences at the scale of evolution enable accurate structure prediction},
author={Lin, Zeming and Akin, Halil and Rao, Roshan and Hie, Brian and Zhu, Zhongkai and Lu, Wenting and dos Santos Costa, Allan and Fazel-Zarandi, Maryam and Sercu, Tom and Candido, Sal and others},
journal={bioRxiv},
year={2022},
publisher={Cold Spring Harbor Laboratory}
}