2.6k citations · 3k across the 23 of their papers we have counts for
16 papers · 1 filter
A clustering-based biased Monte Carlo approach to protein titration curve prediction
Arun V. Sathanur, Nathan A. Baker
In this work, we developed an efficient approach to compute ensemble averages in systems with pairwise-additive energetic interactions between the entities. Methods involving full…
Visualizing biomolecular electrostatics in virtual reality with UnityMol-APBS
Joseph Laureanti, Juan Brandi, Elvis Offor +6
Virtual reality is a powerful tool with the ability to immerse a user within a completely external environment. This immersion is particularly useful when visualizing and analyzing…
Improvements to the APBS biomolecular solvation software suite
Elizabeth Jurrus, Dave Engel, Keith Star +21
The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact i…
Atomic radius and charge parameter uncertainty in biomolecular solvation energy calculations
Xiu Yang, Huan Lei, Peiyuan Gao +3
Atomic radii and charges are two major parameters used in implicit solvent electrostatics and energy calculations. The optimization problem for charges and radii is under-determine…
GIBS: A grand-canonical Monte Carlo simulation program for simulating ion-biomolecule interactions
Dennis G. Thomas, Nathan A. Baker
The ionic environment of biomolecules strongly influences their structure, conformational stability, and inter-molecular interactions.This paper introduces GIBS, a grand-canonical…
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…