Task
Create a README.md that documents ProtPocket using PEA15 as a walkthrough example.
Structure
1. What is ProtPocket
Brief intro — a tool for identifying druggable pockets in AlphaFold protein structures using homodimer comparison.
2. Example Walkthrough: PEA15
Use the PEA15 gene as the running example throughout.
Search
- Search for PEA15 on the homepage
- Show what the result card displays (pLDDT, gap score, disorder delta)
Pocket Analysis
- Explain fpocket analysis on the monomer structure
- Explain fpocket analysis on the homodimer (AlphaFold complex)
- Show how pockets differ between monomer vs homodimer
- Explain the disorder delta and gap score metrics
Molecular Docking
- Walk through selecting a pocket
- Submitting a docking job via AutoDock Vina
- Viewing docked conformations in the Mol* viewer
- Interpreting the results
Notes
- Include screenshots where relevant (placeholders ok)
- Keep language accessible to biologists, not just developers
- Live demo link: https://protpocket.ayushz.me
Task
Create a README.md that documents ProtPocket using PEA15 as a walkthrough example.
Structure
1. What is ProtPocket
Brief intro — a tool for identifying druggable pockets in AlphaFold protein structures using homodimer comparison.
2. Example Walkthrough: PEA15
Use the PEA15 gene as the running example throughout.
Search
Pocket Analysis
Molecular Docking
Notes