122 citations · 449 across the 17 of their papers we have counts for
17 papers
Learned Mappings for Targeted Free Energy Perturbation between Peptide Conformations
Soohaeng Yoo Willow, Lulu Kang, David D. L. Minh
Targeted free energy perturbation uses an invertible mapping to promote configuration space overlap and the convergence of free energy estimates. However, developing suitable mappi…
H-bonds in Crambin: Coherence in an alpha helix
Stanley Nicholson, David Minh, Robert Eisenberg
We applied coherence analysis to molecular dynamics simulations of the plant protein crambin, a thionin storage protein found in Abyssinian cabbage. Coherence analysis was develope…
On the Polarization of Ligands by Proteins
Soohaeng Yoo Willow, Bing Xie, Jason Lawrence +2
Although ligand-binding sites in many proteins contain a high number density of charged side chains that can polarize small organic molecules and influence binding, the magnitude o…
Nonequilibrium path-ensemble averages for symmetric protocols
Trung Hai Nguyen, Van Ngo, João Paulo Castro Zerba +2
According to the nonequilibrium work relations, path-ensembles generated by irreversible processes in which a system is driven out of equilibrium according to a predetermined proto…
Using the Fast Fourier Transform in Binding Free Energy Calculations
Trung Hai Nguyen, Huan-Xiang Zhou, David D. L. Minh
According to implicit ligand theory, the standard binding free energy is an exponential average of the binding potential of mean force (BPMF), an exponential average of the interac…
Alchemical Grid Dock (AlGDock): Binding Free Energy Calculations between Flexible Ligands and Rigid Receptors
David D. L Minh
Alchemical Grid Dock (AlGDock) is open-source software designed to compute the binding potential of mean force (BPMF) - the binding free energy between a flexible ligand and a rigi…