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Title: Potential of mean force calculations of ligand binding to ion channels from Jarzynski's equality and umbrella sampling
Authors: Baştuğ, Turgut
Chen, Po-Chia
Patra, Swarna M.
Kuyucak, Serdar
Keywords: [No Keywords]
Issue Date: 2008
Publisher: Amer Inst Physics
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. (C) 2008 American Institute of Physics.
ISSN: 0021-9606
Appears in Collections:Malzeme Bilimi ve Nanoteknoloji Mühendisliği Bölümü / Department of Material Science & Nanotechnology Engineering
PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection

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