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Ziada S., Braka A., Diharce J., Aci-Seche S. and Bonnet P.

Enhanced Molecular Dynamics Methods Applied to Drug Design Projects.

Enhanced Molecular Dynamics Methods Applied to Drug Design Projects In "Computational Drug Discovery and Design", Methods in molecular biology (Clifton, N.J.), (2018) 1762, 403-426.

par Frapart - publié le

Abstract :

Nobel Laureate Richard P. Feynman stated : "[...] everything that living things do can be understood in terms of jiggling and wiggling of atoms [...]." The importance of computer simulations of macromolecules, which use classical mechanics principles to describe atom behavior, is widely acknowledged and nowadays, they are applied in many fields such as material sciences and drug discovery. With the increase of computing power, molecular dynamics simulations can be applied to understand biological mechanisms at realistic timescales. In this chapter, we share our computational experience providing a global view of two of the widely used enhanced molecular dynamics methods to study protein structure and dynamics through the description of their characteristics, limits and we provide some examples of their applications in drug design. We also discuss the appropriate choice of software and hardware. In a detailed practical procedure, we describe how to set up, run, and analyze two main molecular dynamics methods, the umbrella sampling (US) and the accelerated molecular dynamics (aMD) methods.