ffsshhttiikk 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