152 citations · 157 across the 7 of their papers we have counts for
5 papers · 1 filter
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…
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…
Comparison of free energy methods for molecular systems
F. Marty Ytreberg, Robert H. Swendsen, Daniel M. Zuckerman
We present a detailed comparison of computational efficiency and precision for several free energy difference () methods. The analysis includes both equilibrium and non-equilib…
Simple estimation of absolute free energies for biomolecules
F. Marty Ytreberg, Daniel M. Zuckerman
One reason that free energy difference calculations are notoriously difficult in molecular systems is due to insufficient conformational overlap, or similarity, between the two sta…
Peptide Conformational Equilibria Computed via a Single-Stage Shifting Protocol
F. Marty Ytreberg, Daniel M. Zuckerman
We study the conformational equilibria of two peptides using a novel statistical mechanics approach designed for calculating free energy differences between highly dis-similar conf…