Perspectives on High-Throughput Ligand/Protein Docking With Martini MD Simulations

Paulo C T Souza*, Vittorio Limongelli, Sangwook Wu, Siewert J Marrink*, Luca Monticelli*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

Molecular docking is central to rational drug design. Current docking techniques suffer, however, from limitations in protein flexibility and solvation models and by the use of simplified scoring functions. All-atom molecular dynamics simulations, on the other hand, feature a realistic representation of protein flexibility and solvent, but require knowledge of the binding site. Recently we showed that coarse-grained molecular dynamics simulations, based on the most recent version of the Martini force field, can be used to predict protein/ligand binding sites and pathways, without requiring any a priori information, and offer a level of accuracy approaching all-atom simulations. Given the excellent computational efficiency of Martini, this opens the way to high-throughput drug screening based on dynamic docking pipelines. In this opinion article, we sketch the roadmap to achieve this goal.

Original languageEnglish
Article number657222
Number of pages9
JournalFrontiers in Molecular Biosciences
Volume8
DOIs
Publication statusPublished - 2021

Keywords

  • molecular dynamics
  • coarse-grain
  • ligand-protein
  • protein-protein interaction
  • Martini
  • dynamic docking
  • high-throughput screening
  • drug design

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