PymolDesign: Protein sequence design on PyMOL

Design your protein for given backbone structure on PyMOL!

What's this? PymolDesign = ColabDesign + PymolFold

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

Dependency

• 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/ColabDesign.git@v1.1.0

Usage

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.

Note

This is a repository under development. Issues and PR would be welcomed.

References

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}
}