Biomolecular Design with AI (Perez Lab, UF)

This repo contains all the information needed to get started in Dr. Perez's lab, including sections on AutoDock, Chimera, VMD, BindCraft, AMBER, RFDiffusion, ProteinMPNN, AlphaFold2 and AlphaFold3.

1. Introduction & Background

- AI and structures: from games to molecules
- The protein folding problem & the CASP competition

2. Core Technical Foundations

- Python/Colab notebooks for running AI pipelines
- Introduction to HiPerGator for scalable computing

3. Protein Structure Prediction

- AlphaFold, RoseTTAFold, MSEFold
- Case studies using the Protein Data Bank
- Transformer proteins and memorization issues

4. Protein Design

- Hallucination and move 37
- RFdiffusion and ProteinMPNN
- BindCraft and other emerging methods
- Applications in miniproteins, peptides, and enzyme design

5. Protein Interactions

- AlphaFold competitive binding assays (AF-CBA)
- Modeling interactomes and selectivity

6. Protein Dynamics

- Beyond static folds: ensembles and motion
- BioEMU and AI for conformational states

7. Applications & Frontiers

- Drug discovery, synthetic biology, enzyme design
- Limitations, reproducibility, FAIR practices (Findable, Accessible, Interoperable, Reproducible)

8. Community Challenges: unbiased assessment of methods

- CASP: protein structure prediction
- CAPRI: protein-protein structure prediction
- RNA Puzzles: RNA structure prediction
- BioML Challenge: Bits to binders : designing miniproteins to target cancer cells
- Align Bio: 2025 PETase Tournament
- iGEM projects on campus

To do:

• flow chart showing how to decide which software to use
• folders for each software w/ explanations and instructions
• remember: dont just explain how to use it, explain the big picture and how it works