Advances in molecular dynamics simulations and enhanced sampling methods for the study of protein systems

Raudah Lazim, Donghyuk Suh, Sun Choi

Research output: Contribution to journalReview articlepeer-review

42 Scopus citations

Abstract

Molecular dynamics (MD) simulation is a rigorous theoretical tool that when used efficiently could provide reliable answers to questions pertaining to the structure-function relationship of proteins. Data collated from protein dynamics can be translated into useful statistics that can be exploited to sieve thermodynamics and kinetics crucial for the elucidation of mechanisms responsible for the modulation of biological processes such as protein-ligand binding and protein-protein association. Continuous modernization of simulation tools enables accurate prediction and characterization of the aforementioned mechanisms and these qualities are highly beneficial for the expedition of drug development when effectively applied to structure-based drug design (SBDD). In this review, current all-atom MD simulation methods, with focus on enhanced sampling techniques, utilized to examine protein structure, dynamics, and functions are discussed. This review will pivot around computer calculations of protein-ligand and protein-protein systems with applications to SBDD. In addition, we will also be highlighting limitations faced by current simulation tools as well as the improvements that have been made to ameliorate their efficiency.

Original languageEnglish
Article number6339
Pages (from-to)1-20
Number of pages20
JournalInternational Journal of Molecular Sciences
Volume21
Issue number17
DOIs
StatePublished - 1 Sep 2020

Keywords

  • Binding free energy
  • Enhanced sampling
  • Molecular dynamics simulation
  • Protein-ligand binding affinity
  • Protein-protein interactions

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