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Supervised Molecular Dynamics (SuMD) Approaches in Drug Design

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Rational Drug Design

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1824))

Abstract

Supervised MD (SuMD) is a computational method that enables the exploration of ligand–receptor recognition pathway in a reduced timescale. The performance speedup is due to the incorporation of a tabu-like supervision algorithm on the ligand–receptor approaching distance into a classic molecular dynamics (MD) simulation. SuMD enables the investigation of ligand–receptor binding events independently from the starting position, chemical structure of the ligand (small molecules or peptides), and also from its receptor-binding affinity. The application of SuMD highlights an appreciable capability of the technique to reproduce the crystallographic structures of several ligand–protein complexes and can provide high-quality protein–ligand models of for which yet experimental confirmation of binding mode is not available.

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Author information

Authors and Affiliations

  1. Syngenta Crop Protection AG, Stein, Switzerland

    Davide Sabbadin

  2. Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences , University of Padova, Padova, Italy

    Veronica Salmaso, Mattia Sturlese & Stefano Moro

Authors
  1. Davide Sabbadin
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  2. Veronica Salmaso
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  3. Mattia Sturlese
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  4. Stefano Moro
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Corresponding author

Correspondence to Stefano Moro .

Editor information

Editors and Affiliations

  1. Division of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, Athens, Greece

    Thomas Mavromoustakos

  2. Division of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, Athens, Greece

    Tahsin F. Kellici

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Sabbadin, D., Salmaso, V., Sturlese, M., Moro, S. (2018). Supervised Molecular Dynamics (SuMD) Approaches in Drug Design. In: Mavromoustakos, T., Kellici, T. (eds) Rational Drug Design. Methods in Molecular Biology, vol 1824. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8630-9_17

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  • DOI: https://doi.org/10.1007/978-1-4939-8630-9_17

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8629-3

  • Online ISBN: 978-1-4939-8630-9

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