When to Trigger
Activate this skill when the user mentions:
- Protein folding, AlphaFold, ESMFold, RoseTTAFold
- PDB files, structural analysis, Ramachandran plots
- Molecular docking, binding affinity, binding pockets
- Homology modeling, threading, ab initio structure prediction
- Protein-protein interactions (PPI), interface analysis
- Structural alignment, RMSD, TM-score
- Cryo-EM, X-ray crystallography data interpretation
Step-by-Step Methodology
- Retrieve or predict structure - Search PDB for experimental structures (by UniProt ID or gene name). If unavailable, use AlphaFold DB or run ESMFold. Check pLDDT confidence scores for predicted structures.
- Quality assessment - For experimental structures: check resolution, R-free, and completeness. For predictions: evaluate pLDDT per-residue and PAE (predicted aligned error) matrices.
- Structural analysis - Identify secondary structure elements (helices, sheets, loops). Compute solvent-accessible surface area. Map conserved residues and functional domains.