28 citations · 41 across the 6 of their papers we have counts for
7 papers
Machine-Learned Molecular Surface and Its Application to Implicit Solvent Simulation
Haixin Wei, Zekai Zhao, Ray Luo
Implicit solvent models, such as Poisson-Boltzmann models, play important roles in computational studies of biomolecules. A vital step in almost all implicit solvent models is to d…
Estimating the Roles of Protonation and Electronic Polarization in Absolute Binding Affinity Simulations
Edward King, Ruxi Qi, Han Li +2
Accurate prediction of binding free energies is critical to streamlining the drug development and protein design process. With the advent of GPU acceleration, absolute alchemical m…
Efficient Formulation of Polarizable Gaussian Multipole Electrostatics for Biomolecular Simulations
Haixin Wei, Ruxi Qi, Junmei Wang +3
Molecular dynamics simulations of biomolecules have been widely adopted in biomedical studies. As classical point-charge models continue to be used in routine biomolecular applicat…
Computational Analysis for the Rational Design of Anti-Amyloid Beta (ABeta) Antibodies
D'Artagnan Greene, Theodora Po, Jennifer Pan +2
Alzheimer's Disease (AD) is a neurodegenerative disorder that lacks effective treatment options. Anti-amyloid beta (ABeta) antibodies are the leading drug candidates to treat AD, b…
Exploring A Multi-Scale Method for Molecular Simulations in Continuum Solvent Model: Explicit Simulation of Continuum Solvent As An Incompressible Fluid
Li Xiao, Ray Luo
A multi-scale framework was recently proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute wi…
A Continuum Poisson-Boltzmann Model for Membrane Channel Proteins
Li Xiao, Jianxiong Diao, D Artagnan Greene +2
Membrane proteins constitute a large portion of the human proteome and perform a variety of important functions as membrane receptors, transport proteins, enzymes, signaling protei…
Acceleration of Linear Finite-Difference Poisson-Boltzmann Methods on Graphics Processing Units
Ruxi Qi, Wesley M. Botello-Smith, Ray Luo
Electrostatic interactions play crucial roles in biophysical processes such as protein folding and molecular recognition. Poisson-Boltzmann equation (PBE)-based models have emerged…