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    Steered Molecular Dynamics Simulation in Rational Drug Design
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    • Phuc-Chau Do
      Phuc-Chau Do
      School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City 700000, Vietnam
      More by Phuc-Chau Do
    • Eric H. Lee
      Eric H. Lee
      Department of Medicine and Division of Hematology and Oncology, Loma Linda University Medical Center, Loma Linda, California 92350, United States
      More by Eric H. Lee
    • Ly Le*
      Ly Le
      School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City 700000, Vietnam
      *E-mail: [email protected]
      More by Ly Le
      Orcidhttp://orcid.org/0000-0002-3182-0007
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    Journal of Chemical Information and Modeling

    Cite this: J. Chem. Inf. Model. 2018, 58, 8, 1473–1482
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    https://doi.org/10.1021/acs.jcim.8b00261
    Published July 5, 2018
    Copyright © 2018 American Chemical Society
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    Conventional de novo drug design is time consuming, laborious, and resource intensive. In recent years, emerging in silico approaches have been proven to be critical to accelerate the process of bringing drugs to market. Molecular dynamics (MD) simulations of single molecule and molecular complexes have been commonly applied to achieve accurate binding modes and binding energies of drug-receptor interactions. A derivative of MD, namely, steered molecular dynamics (SMD), has been demonstrated as a promising tool for rational drug design. In this paper, we review various studies over the last 20 years using SMD simulations, thus paving the way to determine the relationship between protein structure and function. In addition, the paper highlights the use of SMD simulation for in silico drug design. We also aim to establish an understanding on the key interactions which play a crucial role in the stabilization of peptide–ligand interfaces, the binding and unbinding mechanism of the ligand–protein complex, the mechanism of ligand translocating via membrane, and the ranking of different ligands on receptors as therapeutic candidates.

    Copyright © 2018 American Chemical Society

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    Cite this: J. Chem. Inf. Model. 2018, 58, 8, 1473–1482
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    https://doi.org/10.1021/acs.jcim.8b00261
    Published July 5, 2018
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