18 citations · 25 across the 4 of their papers we have counts for
5 papers
Folding is Not Required for Bilayer Insertion: Replica Exchange Simulations of an a-Helical Peptide with an Explicit Lipid Bilayer
Hugh Nymeyer, Thomas B. Woolf, Angel E. Garcia
We implement the replica exchange molecular dynamics algorithm to study the interactions of a model peptide (WALP-16) with an explicitly represented DPPC membrane bilayer. We obser…
Rapid Determination of Multiple Reaction Pathways in Molecular Systems: The Soft-Ratcheting Algorithm
Daniel M. Zuckerman, Thomas B. Woolf
We discuss the ``soft-ratcheting'' algorithm which generates targeted stochastic trajectories in molecular systems with scores corresponding to their probabilities. The procedure,…
Systematic Finite-Sampling Inaccuracy in Free Energy Differences and Other Nonlinear Quantities
Daniel M. Zuckerman, Thomas B. Woolf
Systematic inaccuracy is inherent in any computational estimate of a non-linear average, such as the free energy difference (Delta-F) between two states or systems, because of the…
Dependence of Sidechain Rotamer Preference on Backbone Conformation: Relative Free Energy Calculations for Valine and Leucine
John G. Pearson, Thomas B. Woolf
Three dimensional relative free energy calculations are used to directly calculate the dependence of the preferred sidechain rotamers for valine and leucine on the conformation of…
Extrapolative Analysis of Fast-Switching Free Energy Estimates in a Molecular System
Daniel M. Zuckerman, Thomas B. Woolf
We perform an extrapolative analysis of "fast-growth" free-energy-difference (DF) estimates of a computer-modeled, fully-solvated ethane<->methanol transformation. The results sugg…