User Guide¶
REvoDesign is a PyMOL plugin for semi-rational enzyme redesign. It integrates structural analysis, evolutionary data, and computational mutagenesis into a graphical workflow.
Workflow¶
REvoDesign's tabbed interface follows the stages of a rational design pipeline:
| Stage | Tab | What you do |
|---|---|---|
| Prepare | Prepare | Load structure, detect binding pockets and surface-exposed hotspots |
| Mutate | Mutate | Generate virtual saturation mutagenesis libraries under PSSM constraints |
| Evaluate | Evaluate | Visually inspect and accept/reject mutants in the MutantTree |
| Cluster | Cluster | Reduce library size via sequence-based clustering with optional Rosetta energy scoring |
| Visualize | Visualize | Cross-screen with external tools (ddG, ESM-1v) and display experimental data on structure |
| Interact | Interact | Explore co-evolved residue pairs via GREMLIN MRF and design combinatorial mutants |
| Socket | Socket | Collaborate with other users on shared sessions |
| Config | Config | Inspect and edit configuration files |
Contents¶
- Installation — Detailed Package Manager GUI setup, system requirements, self-upgrade, and configuration reset.
- Interface Overview — UI zones, drop-down menus, language switching, and configuration management.
- Workflow Tutorial — Step-by-step walkthrough using CYP450 (1SUO) from pocket detection through co-evolution analysis.
- Cluster Methods — Available clustering algorithms and how to choose between them.
- OpenKinetics — Using the OpenKinetics API for external scoring of mutants.
- Advanced Design Tools — Profile Design heatmap, ThermoMPNN stability prediction, and RFdiffusion backbone generation.
- Programmatic Mutagenesis — Generate mutant PDBs from Python for downstream MD, docking, and free energy calculations.
Quick Reference¶
| I want to... | Go to |
|---|---|
| Install REvoDesign for the first time | Installation |
| Understand the UI layout | Interface Overview |
| Follow a complete design workflow | Workflow Tutorial |
| Pick a clustering method | Cluster Methods |
| Use the Profile Design heatmap | Advanced Design Tools |
| Predict stability with ThermoMPNN | Advanced Design Tools |
| Run RFdiffusion backbone design | Advanced Design Tools |
| Generate mutant PDBs for MD/docking | Programmatic Mutagenesis |
| Install Rosetta for energy scoring | Rosetta Integration |
| Set up the PSSM/GREMLIN server | PSSM/GREMLIN Server |