3 papers
physics.comp-ph2008★ 1 cited
Reducing the Bias and Uncertainty of Free Energy Estimates by Using Regression to Fit Thermodynamic Integration Data
Conrad Shyu, F. Marty Ytreberg
This report presents the application of polynomial regression for estimating free energy differences using thermodynamic integration. We employ linear regression to construct a pol…
physics.bio-ph2007★ 1 cited
Absolute FKBP binding affinities obtained via non-equilibrium unbinding simulations
F. Marty Ytreberg
We compute absolute binding affinities for two ligands bound to the FKBP protein using non-equilibrium unbinding simulations. The methodology is straight-forward, requiring little…
physics.bio-ph2007
Demonstrated convergence of the equilibrium ensemble for a fast united-residue protein model
F. Marty Ytreberg, Svetlana Kh. Aroutiounian, Daniel M. Zuckerman
Due to the time-scale limitations of all-atom simulation of proteins, there has been substantial interest in coarse-grained approaches. Some methods, like "Resolution Exchange," [E…