Enhanced Molecular Dynamics Methods Applied to Drug Design Projects

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.
Document type :
Journal articles
Complete list of metadatas

https://hal.archives-ouvertes.fr/hal-01966502
Contributor : Isabelle Frapart <>
Submitted on : Friday, December 28, 2018 - 1:42:37 PM
Last modification on : Saturday, December 29, 2018 - 1:12:56 AM

Identifiers

  • HAL Id : hal-01966502, version 1

Collections

Citation

Sonia Ziada, Abdennour Braka, Julien Diharce, Samia Aci-Seche, Pascal Bonnet. Enhanced Molecular Dynamics Methods Applied to Drug Design Projects. Methods in Molecular Biology, Humana Press/Springer Imprint, 2018, 1762, pp.403-426. ⟨hal-01966502⟩

Share

Metrics

Record views

23