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Tag Archives: free-energy
AdK apo PMF

AdK apo PMF

The enzyme adenylate kinase (AdK) undergoes a large hinge-like motion. In 2009, we studied the conformational transition between open and closed E. coli AdK without substrate, i.e. “apo AdK”, with a variety of computational methods. As part of the study we also produced a free energy landscape (a potential of mean force or PMF) as a function of the two domain angles. Here we make the data of the underlying free energy landscape available to other researchers so that they can use them in their own research.

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Summer Book Club 2014: Molecular Simulations and Theory

Summer Book Club 2014: Molecular Simulations and Theory

This summer’s Lab Book Club is designed to provide a thorough review of fundamental concepts for understanding biomolecular simulation and, in particular,molecular dynamics simulations (MD). The material is primarily based on chapters from Statistical Mechanics: Theory and Molecular Simulation by Mark Tuckerman.

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Ian Kenney

Ian Kenney

Ian Kenney is a PhD graduate student in Physics. He started his PhD in 2017 but was working in the lab as an undergraduate since 2015. His current primary interest is in quantitative simulations of transporter proteins. He is also working on methods and protocols to accurately calculate solvation energies of small and drug-like molecules.

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Sampling macromolecular transitions

Sampling macromolecular transitions

While equilibrium MD is considered the most robust approach to simulating macromolecular conformational changes, conformational transitions are rare events that take place on much faster timescales than the waiting times spent in metastable equilibrium states. Equilibrium simulations thus spend relatively little time sampling actual transition events. Fast transition path sampling methods seek to mitigate the rare event sampling problem, though the full extent to which biased or coarse-grained approaches can replicate physical ensembles of transitions is unknown.

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