On the Use of Molecular Dynamics Receptor Conformations for Virtual Screening

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 819)

Abstract

Receptors are inherently dynamic and this flexibility is important to consider when constructing a model of molecular association. Conformations from molecular dynamics simulations, a well-established method for examining protein dynamics, can be used in virtual screening to account for flexibility in structure-based drug discovery. Different receptor configurations influence docking results. Molecular dynamics simulations can provide snapshots that improve virtual screening predictive power over known crystal structures, most likely as a result of sampling more relevant receptor conformations. Here we highlight some details and nuances of using such snapshots and evaluating them for predictive performance.

Key words

Docking Receptor structures X-ray crystallography Molecular dynamics 

Notes

Acknowledgments

The authors would like to thank the members of the McCammon research group for useful discussions. This work was supported in part by the National Science Foundation, the National Institutes of Health, Howard Hughes Medical Institute, the San Diego Supercomputer Center, the Center for Theoretical Biological Physics and the National Biomedical Computational Resource.

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Department of Chemistry and Biochemistry, Center for Theoretical Biological PhysicsUniversity of California, San DiegoLa JollaUSA
  2. 2.Department of Medicinal Chemistry, College of Pharmacy, The Henry Eyring Center for Theoretical ChemistryUniversity of UtahSalt Lake CityUSA
  3. 3.Howard Hughes Medical Institute, Departments of Chemistry and Biochemistry and Pharmacology, Center for Theoretical Biological PhysicsUniversity of California, San DiegoLa JollaUSA

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