structural-biology

name	structural-biology
description	3D structure of biological molecules
license	MIT
compatibility	opencode
metadata	{"audience":"structural biologists, biochemists, researchers","category":"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

# 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