209 citations · 499 across the 12 of their papers we have counts for
12 papers
Computational Estimates of Binding Affinities for Estrogen Receptor Isoforms in Rainbow Trout
Conrad Shyu, Celeste J. Brown, F. Marty Ytreberg
Molecular dynamics simulations were used to determine the binding affinities between between the hormone 17 beta-estradiol (E2) and different estrogen receptor (ER) isoforms in the…
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…
Accurate Estimation of Solvation Free Energy Using Polynomial Fitting Techniques
Conrad Shyu, F. Marty Ytreberg
This report details an approach to improve the accuracy and precision of free energy difference estimates using thermodynamic integration data (slope of the free energy with respec…
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…
A "black-box" re-weighting analysis can correct flawed simulation data, after the fact
F. Marty Ytreberg, Daniel M. Zuckerman
There is a great need for improved statistical sampling in a range of physical, chemical and biological systems. Even simulations based on correct algorithms suffer from statistica…