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

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.
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https://hal-cnrs.archives-ouvertes.fr/hal-03863186
Contributor : Paulo Telles de Souza Connect in order to contact the contributor
Submitted on : Monday, November 21, 2022 - 12:36:51 PM
Last modification on : Saturday, November 26, 2022 - 3:52:05 AM

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Paulo Souza, Vittorio Limongelli, Sangwook Wu, Siewert Marrink, Luca Monticelli. Perspectives on High-Throughput Ligand/Protein Docking With Martini MD Simulations. Frontiers in Molecular Biosciences, 2021, 8, ⟨10.3389/fmolb.2021.657222⟩. ⟨hal-03863186⟩

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