Applications of the NRGsuite and the Molecular Docking Software FlexAID in Computational Drug Discovery and Design
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 wordsComputer-aided drug design Binding mode prediction Lead identification Molecular docking Molecular flexibility Molecular recognition Protein–ligand complex
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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