2.6k citations · 3k across the 23 of their papers we have counts for
5 papers · 1 filter
PB-AM: An Open-Source, Fully Analytical Linear Poisson-Boltzmann Solver
Lisa E. Feldberg, David H. Brookes, Eng-Hui Yap +3
We present the open source distributed software package Poisson-Boltzmann Analytical Method (PB-AM), a fully analytical solution to the linearized Poisson Boltzmann equation, for m…
Bayesian Model Averaging for Ensemble-Based Estimates of Solvation Free Energies
Luke J. Gosink, Christopher C. Overall, Sarah M. Reehl +3
This paper applies the Bayesian Model Averaging (BMA) statistical ensemble technique to estimate small molecule solvation free energies. There is a wide range of methods available…
Data-driven parameterization of the generalized Langevin equation
Huan Lei, Nathan Baker, Xiantao Li
We present a data-driven approach to determine the memory kernel and random noise in generalized Langevin equations. To facilitate practical implementations, we parameterize the ke…
Multi-shell model of ion-induced nucleic acid condensation
Igor S. Tolokh, Aleksander Drozdetski, Lois Pollack +2
We present a semi-quantitative model of condensation of short nucleic acid (NA) duplexes induced by tri-valent cobalt(III) hexammine (CoHex) ions. The model is based on partitionin…
Continuum Electrostatics Approaches to Calculating ps and s in Proteins
Marilyn R. Gunner, Nathan A. Baker
Proteins change their charge state through protonation and redox reactions as well as through binding charged ligands. The free energy of these reactions are dominated by solvation…