Applications of the NRGsuite and the Molecular Docking Software FlexAID in Computational Drug Discovery and Design

  • Louis-Philippe Morency
  • Francis Gaudreault
  • Rafael Najmanovich
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1762)

Abstract

Docking simulations help us understand molecular interactions. Here we present a hands-on tutorial to utilize FlexAID (Flexible Artificial Intelligence Docking), an open source molecular docking software between ligands such as small molecules or peptides and macromolecules such as proteins and nucleic acids. The tutorial uses the NRGsuite PyMOL plugin graphical user interface to set up and visualize docking simulations in real time as well as detect and refine target cavities. The ease of use of FlexAID and the NRGsuite combined with its superior performance relative to widely used docking software provides nonexperts with an important tool to understand molecular interactions with direct applications in structure-based drug design and virtual high-throughput screening.

Key words

Computer-aided drug design Binding mode prediction Lead identification Molecular docking Molecular flexibility Molecular recognition Protein–ligand complex 

Notes

Acknowledgments

R.J.N. is part of PROTEO (the Québec network for research on protein function, structure, and engineering) and GRASP (Groupe de Recherche Axé sur la Structure des Protéines). The authors would like to thank the users of FlexAID and the NRGsuite for numerous bug reports and feedbacks, thus contributing to their development, and Florence Min for critical reading of the manuscript.

Funding: L.P.M. is the recipient of a Ph.D. fellowship from the Fonds de Recherche du Québec—Nature et Technologies (FRQ-NT).

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Copyright information

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

Authors and Affiliations

  • Louis-Philippe Morency
    • 1
  • Francis Gaudreault
    • 2
  • Rafael Najmanovich
    • 1
  1. 1.Department of Pharmacology and Physiology, Faculty of MedicineUniversité de MontréalMontréalCanada
  2. 2.National Research Council CanadaOttawaCanada

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