Wednesday
Overview
Wednesday focuses on advanced structure prediction and protein design. You’ll compare AlphaFold3 and Chai-1 for complex predictions (multimers, ligands, ions), then dive into RFdiffusion for de novo protein design including binder generation and symmetric oligomers.
By the end of Wednesday, you’ll be able to:
- Compare AlphaFold3 and Chai-1 across monomers, multimers, and protein-ligand complexes, and articulate their trade-offs.
- Run RFdiffusion to generate unconditional monomers and interpret the resulting backbones.
- Use motif scaffolding and hotspot residues to steer RFdiffusion toward a target binding interface.
- Design symmetric oligomers and understand when symmetry is a useful design constraint.
- Evaluate a designed backbone using confidence metrics and decide whether it’s worth sequence-designing and predicting.
Modules
| Module | Topic | Description |
|---|---|---|
| 1. AlphaFold3 vs. Chai-1 | Comparing Next-Gen Predictors | Compare AF3 and Chai-1 on monomers, multimers, and protein-ligand complexes |
| 2. RFdiffusion | Advanced Protein Design | Design unconditional monomers, motif scaffolds, binders, and symmetric oligomers using RFdiffusion |