BayesWHAM: A Bayesian approach for free energy estimation, reweighting, and uncertainty quantification in the weighted histogram analysis method

Thermal Unthreading of the Lasso Peptides Astexin-2 and Astexin-3

(2016) Caitlin D. Allen et al.   ACS Chemical Biology

Accelerating the weighted histogram analysis method by direct inversion in the iterative subspace

(2016) Cheng Zhang et al.   MOLECULAR SIMULATION

Distributions of experimental protein structures on coarse-grained free energy landscapes

(2015) Kannan Sankar et al.   JOURNAL OF CHEMICAL PHYSICS

Systematic characterization of protein folding pathways using diffusion maps: Application to Trp-cage miniprotein

(2015) Sang Beom Kim et al.   JOURNAL OF CHEMICAL PHYSICS

Nonlinear Machine Learning of Patchy Colloid Self-Assembly Pathways and Mechanisms

(2014) Andrew W. Long et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Activation pathway of Src kinase reveals intermediate states as targets for drug design

(2014) Diwakar Shukla et al.   Nature Communications

Rapid Exploration of Configuration Space with Diffusion-Map-Directed Molecular Dynamics

(2013) Wenwei Zheng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Discovery and Characterization of an Isopeptidase That Linearizes Lasso Peptides

(2013) Mikhail O. Maksimov et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Theory of binless multi-state free energy estimation with applications to protein-ligand binding

(2012) Zhiqiang Tan et al.   JOURNAL OF CHEMICAL PHYSICS

Bayesian Estimation of Free Energies From Equilibrium Simulations

(2012) Michael Habeck   PHYSICAL REVIEW LETTERS

Nonlinear dimensionality reduction in molecular simulation: The diffusion map approach

(2011) Andrew L. Ferguson et al.   CHEMICAL PHYSICS LETTERS

On two possible definitions of the free energy for collective variables

(2011) C. Hartmann et al.   European Physical Journal-Special Topics

Integrating diffusion maps with umbrella sampling: Application to alanine dipeptide

(2011) Andrew L. Ferguson et al.   JOURNAL OF CHEMICAL PHYSICS

Polymer reversal rate calculated via locally scaled diffusion map

(2011) Wenwei Zheng et al.   JOURNAL OF CHEMICAL PHYSICS

Convergence and error estimation in free energy calculations using the weighted histogram analysis method

(2011) Fangqiang Zhu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

An Experimental and Computational Investigation of Spontaneous Lasso Formation in Microcin J25

(2010) Andrew L. Ferguson et al.   BIOPHYSICAL JOURNAL

g_wham—A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates

(2010) Jochen S. Hub et al.   Journal of Chemical Theory and Computation

Systematic determination of order parameters for chain dynamics using diffusion maps

(2010) A. L. Ferguson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Making sense of the Legendre transform

(2009) R. K. P. Zia et al.   AMERICAN JOURNAL OF PHYSICS

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

(2009) Massimiliano Bonomi et al.   COMPUTER PHYSICS COMMUNICATIONS

Deconstructing the Native State: Energy Landscapes, Function, and Dynamics of Globular Proteins

(2009) Pavel I. Zhuravlev et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Statistically optimal analysis of samples from multiple equilibrium states

(2008) Michael R. Shirts et al.   JOURNAL OF CHEMICAL PHYSICS

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

On the Molecular Mechanism of Drug Intercalation into DNA: A Simulation Study of the Intercalation Pathway, Free Energy, and DNA Structural Changes

(2008) Arnab Mukherjee et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY