How are 3D macromolecular structures obtained?
  1. Empirical determination

    1. X-ray crystallography (83% of PDB entries)

    2. Solution NMR spectroscopy (15% of PDB entries)
        Limited to <=30 kD.

    3. Electron microscopy or diffraction (0.3% of PDB entries)

  2. Theory

    1. Comparative ("Homology") Modeling.
      1. Need for empirical template limits it to ~20% of cases.
      2. Errors in sequence alignment of target with template give errors in the model.
      3. Insertions, deletions cannot be reliably modeled.
      4. Can be reliable for main chain fold, surface/buried; side-chain positions unreliable.
      5. ~70% success when >=60% sequence identity.
      6. ~10% failure rate even when >=90% sequence identity.

    2. Ab initio theoretical modeling.
      • Secondary structure: ~70% accuracy.
      • Tertiary structure: accuracy too low for most purposes:
          "For roughly 40% of proteins shorter than 150 amino acids [<15 kD] ..., one of the five most commonly recurring models ... has sufficient global similarity to the true structure to recognize it ...." (Baker & Sali, 2001).
      • Biannual competitions: CASP.
      • Docking competition: CAPRI.

by Eric Martz, University of Massachusetts, July 2003


Further Reading: