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Molecular Dynamics Simulation and Prediction of Druggable Binding Sites

  • Tianhua Feng
  • Khaled Barakat
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1762)

Abstract

Binding site identification and druggability evaluation are two essential steps in structure-based drug design. A druggable binding site tends to have high binding affinity to drug-like molecules. Predicting such sites can have a significant impact on a drug design campaign. This chapter focuses on summarizing the different methods that are used to predict druggable binding sites. The chapter also discusses the importance of including protein flexibility in the search process and the use of molecular dynamics simulations to address this aspect. Case studies from the literature are also summarized and discussed. We hope that this chapter would provide an overview on the different methods employed in binding site identification evaluation.

Key words

Conformational ensemble Cosolvent molecular dynamic simulation Druggability Hot spot Protein flexibility 

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Faculty of Pharmacy and Pharmaceutical SciencesUniversity of AlbertaEdmontonCanada

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