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Protein docking and complementarity.

B K Shoichet1, I D Kuntz

  • 1Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-0446.

Journal of Molecular Biology
|September 5, 1991
PubMed
Summary
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This study presents a rigid body docking method that accurately predicts protein-protein complex structures using unbound protein conformations. Simple interface scoring failed, but energy minimization showed promise for identifying correct complex models.

Area of Science:

  • Computational biology
  • Structural biology
  • Biophysics

Background:

  • Predicting protein-protein complex structures is challenging due to topographical and thermodynamic complexity.
  • Previous methods often relied on rigid body searches using crystal conformations.

Purpose of the Study:

  • To evaluate a rigid body docking method for predicting protein-protein complex structures.
  • To assess the effectiveness of various scoring functions in distinguishing correct from incorrect models.

Main Methods:

  • Employed a rigid body docking approach using both bound and unbound protein conformations.
  • Generated structures for three known protein complexes.
  • Evaluated interface complementarity using surface area burial, solvation free energy, packing, and mechanism-based filtering.

Related Experiment Videos

  • Assessed total interaction energy and electrostatic interaction energy.
  • Utilized energy minimization to differentiate true and false positives.

    • Main Results:

    • The docking method accurately regenerated crystallographic complex geometries using unbound conformations.
    • Simple interface scoring methods could not distinguish between correct and incorrect models.
    • Energy minimization showed better discrimination, though energy differences were small.
    • Lowest energy docked structures were within 5 Å root-mean-square deviation of crystallographic structures.

    Conclusions:

    • Rigid body docking using unbound conformations is a viable tool for predicting protein complex structures.
    • Energy minimization, while imperfect, offers a more reliable scoring approach than simple interface complementarity.
    • Further research is needed to establish the reliability of energy calculations in macromolecular systems.