REvoDesign¶
A PyMOL plugin for enzyme redesign — REvoDesign combines structural and evolutionary information to help protein designers engineer enzymes with greater confidence and less manual effort.
Key Features¶
- Surface Residue Analysis — Identify solvent-accessible residues and design pockets around substrates and cofactors with customizable cutoffs.
- Mutant Loading & Scoring — Load designable mutants from PSSM-like CSV tables with configurable rejections and preferences.
- Human Knowledge Supervision — Visually inspect and curate mutants directly inside the PyMOL interface.
- Sequence Clustering — Reduce mutant set size for low-throughput wet-lab validation using one of several built-in clustering methods.
- Co-Evolution Analysis — Search for co-evolved residue pairs via the GREMLIN Markov random field profile.
- Visualization — Color structures by mutation scores, generate PyMOL sessions, and export results.
- Multi-User Collaboration — Share designs across a team with the socket broadcast system.
Quick Start¶
conda create -n revodesign python=3.12 -y
conda activate revodesign
conda install -c conda-forge pymol-open-source pyqt=5 -y
Then launch PyMOL, open Plugin > Plugin Manager > Install New Plugin, choose Install from PyMOLWiki or any URL, and paste the Package Manager URL:
https://gist.githubusercontent.com/YaoYinYing/c1e8bfe0fc0b9c60bf49ea04a550a044/raw/REvoDesign_PyMOL.py
Click Fetch, confirm, and use the REvoDesign Package Manager to install the main program.
Learn More¶
| Link | What you will find |
|---|---|
| Getting Started | Prerequisites, install, first launch |
| User Guide | Walkthroughs for each workflow stage |
| API Reference | Full API documentation |
| GitHub Repository | Source code, issues, discussions |