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beita6969 / protein-structure

Analyzes protein 3D structures, performs homology modeling, interprets AlphaFold predictions, conducts molecular docking, and evaluates protein-ligand interactions; trigger when users ask about PDB files, folding, binding sites, or structural biology.

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SKILL.md
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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

  1. 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.
  2. Quality assessment - For experimental structures: check resolution, R-free, and completeness. For predictions: evaluate pLDDT per-residue and PAE (predicted aligned error) matrices.
  3. Structural analysis - Identify secondary structure elements (helices, sheets, loops). Compute solvent-accessible surface area. Map conserved residues and functional domains.
  4. Binding site identification - Use fpocket, SiteMap, or DoGSiteScorer for pocket detection. Cross-reference with known ligand binding from PDBe or BindingDB.
  5. Molecular docking - Recommend AutoDock Vina, GNINA, or Glide. Define grid box around binding site. Report binding energy (kcal/mol) and key interactions (H-bonds, hydrophobic, pi-stacking).
  6. Structural comparison - Align structures using TM-align or FATCAT. Report RMSD and TM-score. Identify conformational changes between states.
  7. Visualization guidance - Recommend PyMOL, ChimeraX, or Mol* for rendering. Specify coloring schemes (by chain, B-factor, electrostatics, or conservation).

Key Databases and Tools

  • PDB / PDBe - Experimental protein structures
  • AlphaFold DB - AI-predicted structures for UniProt entries
  • UniProt - Protein sequences, domains, and annotations
  • InterPro / Pfam - Domain classification
  • BindingDB / ChEMBL - Binding affinity data
  • RCSB PDB REST API - Programmatic structure queries
  • PDBe-KB - Aggregated structural annotations

Output Format

  • Report structures with PDB ID, resolution, method, and chain identifiers.
  • Binding energies in kcal/mol with interaction fingerprints.
  • Structural alignments with RMSD (in Angstroms) and TM-score.
  • Residue numbering must match the canonical UniProt sequence or PDB SEQRES.
  • Include PyMOL/ChimeraX commands for reproducing visualizations.

Quality Checklist

  • [ ] Structure source and method (X-ray, cryo-EM, NMR, predicted) clearly stated
  • [ ] Resolution or confidence metric (pLDDT) reported
  • [ ] Binding site residues listed with chain and numbering
  • [ ] Docking results include top poses and interaction details
  • [ ] Limitations of predicted structures acknowledged where relevant
  • [ ] All PDB IDs verified as valid and current
  • [ ] Biological assembly vs. asymmetric unit distinguished