Exploring the free-energy landscapes of biological systems with steered molecular dynamics
نویسندگان
چکیده
منابع مشابه
Exploring the free-energy landscapes of biological systems with steered molecular dynamics.
We perform steered molecular dynamics (SMD) simulations and use the Brownian dynamics fluctuation-dissipation-theorem (BD-FDT) to accurately compute the free-energy profiles for several biophysical processes of fundamental importance: hydration of methane and cations, binding of benzene to T4-lysozyme L99A mutant, and permeation of water through aquaglyceroporin. For each system, the center-of-...
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Steered molecular dynamics (SMD) induces unbinding of ligands and conformational changes in biomolecules on time scales accessible to molecular dynamics simulations. Time-dependent external forces are applied to a system, and the responses of the system are analyzed. SMD has already provided important qualitative insights into biologically relevant problems, as demonstrated here for application...
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ژورنال
عنوان ژورنال: Physical Chemistry Chemical Physics
سال: 2011
ISSN: 1463-9076,1463-9084
DOI: 10.1039/c0cp02799e