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Supervised Molecular Dynamics (SuMD) Approaches in Drug Design

  • Davide Sabbadin
  • Veronica Salmaso
  • Mattia Sturlese
  • Stefano Moro
Protocol
Part of the Methods in Molecular Biology book series (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.

Key words

Ligand–protein binding Peptide–protein binding Recognition pathway Molecular dynamics Supervised molecular dynamics Meta-binding site 

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Copyright information

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

Authors and Affiliations

  • Davide Sabbadin
    • 1
  • Veronica Salmaso
    • 2
  • Mattia Sturlese
    • 2
  • Stefano Moro
    • 2
  1. 1.Syngenta Crop Protection AGSteinSwitzerland
  2. 2.Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences University of PadovaPadovaItaly

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