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Computational Drug Discovery and Design pp 367–388Cite as

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

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Part of the book series: Methods in Molecular Biology ((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.

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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).

Author information

Authors and Affiliations

  1. Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada

    Louis-Philippe Morency & Rafael Najmanovich

  2. National Research Council Canada, Ottawa, Canada

    Francis Gaudreault

Authors
  1. Louis-Philippe Morency
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  2. Francis Gaudreault
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  3. Rafael Najmanovich
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Corresponding author

Correspondence to Rafael Najmanovich .

Editor information

Editors and Affiliations

  1. Department of Basic and Applied Sciences, Dayananda Sagar University, Bangalore, KA, India

    Mohini Gore

  2. Department of Biotechnology, Shivaji University, Kolhapur, MH, India

    Umesh B. Jagtap

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Morency, LP., Gaudreault, F., Najmanovich, R. (2018). Applications of the NRGsuite and the Molecular Docking Software FlexAID in Computational Drug Discovery and Design. In: Gore, M., Jagtap, U. (eds) Computational Drug Discovery and Design. Methods in Molecular Biology, vol 1762. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7756-7_18

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  • DOI: https://doi.org/10.1007/978-1-4939-7756-7_18

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7755-0

  • Online ISBN: 978-1-4939-7756-7

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