structural-biology

## What I do - Determine 3D structures of biomolecules - Analyze protein folding and conformation - Study molecular interactions - Interpret structural data - Model protein-ligand complexes - Predict protein structure ## When to use me - When analyzing protein structures - When studying molecular interactions - When interpreting PDB data - When predicting protein structure - When studying enzyme mechanisms - When designing drugs ## Key Concepts ### Structure Determination **Experimental Methods** - X-ray crystallography: Atomic resolution - Nuclear Magnetic Resonance (NMR): Solution structure - Cryo-electron microscopy: Large complexes - Electron diffraction: Small molecules ### Protein Structure Levels ```python # Protein structure hierarchy structure_levels = { 'primary': 'Linear amino acid sequence', 'secondary': 'Local structural motifs', 'tertiary': '3D folding of single chain', 'quaternary': 'Multi-subunit assembly' } # Secondary structure secondary_elements = { 'alpha_helix': '3.6 residues/turn, i to i+4 H-bond', 'beta_sheet': 'Interstrand H-bonds, parallel or antiparallel', 'turns': 'Reverse direction, often Gly, Pro' } ``` ### Structure Analysis - Ramachandran plot: Allowed φ, ψ angles - Contact maps: Residue interactions - RMSD: Structure alignment - DALI: Fold similarity - PISA: Interface analysis ### Protein-Ligand Interactions - Hydrogen bonds - Hydrophobic interactions - Electrostatic interactions - Van der Waals forces - π-stacking - Cation-π interactions ### Structure Prediction - Homology modeling - Threading - Ab initio folding - AlphaFold, RoseTTAFold - Rosetta