Potential of mean force calculations of ligand binding to ion channels from Jarzynski's equality and umbrella sampling

  • Batuǧ T
  • Chen P
  • Patra S
 et al. 
  • 108

    Readers

    Mendeley users who have this article in their library.
  • 55

    Citations

    Citations of this article.

Abstract

Potential of mean force (PMF) calculations provide a reliable method for determination of the absolute binding free energies for protein-ligand systems. The common method used for this purpose -- umbrella sampling with weighted histogram analysis -- is computationally very laborious, which limits its applications. Recently, a much simpler alternative for PMF calculations has become available, namely, using Jarzynski's equality in steered molecular dynamics simulations. So far, there have been a few comparisons of the two methods and mostly in simple systems that do not reflect the complexities of protein-ligand systems. Here, we use both methods to calculate the PMF for ion permeation and ligand binding to ion channels. Comparison of results indicate that Jarzynski's method suffers from relaxation problems in complex systems and would require much longer simulation times to yield reliable PMFs for protein-ligand systems.

Get free article suggestions today

Mendeley saves you time finding and organizing research

Sign up here
Already have an account ?Sign in

Find this document

Authors

  • Turgut Batuǧ

  • Po Chia Chen

  • Swarna M. Patra

  • Serdar Kuyucak

Cite this document

Choose a citation style from the tabs below

Save time finding and organizing research with Mendeley

Sign up for free