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Flexible receptor docking for drug discovery.

Chung F Wong1

  • 1a University of Missouri-St. Louis, Department of Chemistry and Biochemistry , 1 University Boulevard, St. Louis, MO 63121, USA +1 31 4516 5318 ; wongch@umsl.edu.

Expert Opinion on Drug Discovery
|August 28, 2015
PubMed
Summary

Ensemble docking enhances molecular docking by incorporating receptor flexibility, improving virtual screening accuracy for drug discovery. Careful ensemble selection and scoring methods are key to identifying more true drug candidates.

Keywords:
Boltzmann-enhanced discrimination of receiver operating characteristicsconformational transition pathenrichment factorensemble dockingmolecular dynamicsnormal modereplica-exchange simulationsimulated annealing cycling

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Area of Science:

  • Computational Chemistry
  • Structural Biology
  • Drug Discovery

Background:

  • Molecular docking is crucial for virtual screening but rigid receptor models yield false negatives.
  • Flexible receptor docking addresses limitations of rigid models, improving compound identification.
  • Ensemble docking offers an approximate yet cost-effective approach to simulate receptor flexibility.

Purpose of the Study:

  • To review ensemble docking as a method for flexible receptor docking.
  • To outline key features and recent advances in ensemble docking.
  • To identify areas for improvement in ensemble docking for drug discovery.

Main Methods:

  • Review of ensemble docking methodologies.
  • Discussion of structural ensemble generation (experimental, modeling, simulations).
  • Analysis of strategies for optimizing ensemble size and content.

Main Results:

  • Ensemble docking is a popular approach for high-throughput virtual screening.
  • Structural ensembles can be generated through various methods, with judicious selection improving performance.
  • Reducing ensemble size and removing poorly binding structures can enhance active identification.

Conclusions:

  • Ensemble docking is a valuable tool for flexible receptor docking, particularly in high-throughput screening.
  • Optimizing ensemble composition and size impacts computational cost and accuracy.
  • Further research is needed in scoring and ranking methods to maximize true positives in ensemble docking.