TABI-PB 2.0: An Improved Version of the Treecode-Accelerated Boundary Integral Poisson-Boltzmann Solver

A GPU-accelerated fast multipole method based on barycentric Lagrange interpolation and dual tree traversal

(2021) Leighton Wilson et al.   COMPUTER PHYSICS COMMUNICATIONS

Comparison of the MSMS and NanoShaper molecular surface triangulation codes in the TABI Poisson–Boltzmann solver

(2021) Leighton Wilson et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Computational modeling of protein conformational changes - Application to the opening SARS-CoV-2 spike

(2021) Anna Kucherova et al.   JOURNAL OF COMPUTATIONAL PHYSICS

On preconditioning the treecode-accelerated boundary integral (TABI) Poisson-Boltzmann solver

(2018) Jiahui Chen et al.   JOURNAL OF COMPUTATIONAL PHYSICS

An implicit boundary integral method for computing electric potential of macromolecules in solvent

(2018) Yimin Zhong et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Refinement and Analysis of the Mature Zika Virus Cryo-EM Structure at 3.1 Å Resolution

(2018) Madhumati Sevvana et al.   STRUCTURE

NanoShaper–VMD interface: computing and visualizing surfaces, pockets and channels in molecular systems

(2018) Sergio Decherchi et al.   BIOINFORMATICS

A Computational Assay that Explores the Hemagglutinin/Neuraminidase Functional Balance Reveals the Neuraminidase Secondary Site as a Novel Anti-Influenza Target

(2018) Rommie E. Amaro et al.   ACS Central Science

Improvements to the APBS biomolecular solvation software suite

(2017) Elizabeth Jurrus et al.   PROTEIN SCIENCE

An Adaptive, Finite Difference Solver for the Nonlinear Poisson-Boltzmann Equation with Applications to Biomolecular Computations

(2016) Mohammad Mirzadeh et al.   Communications in Computational Physics

Between Algorithm and Model: Different Molecular Surface Definitions for the Poisson-Boltzmann Based Electrostatic Characterization of Biomolecules in Solution

(2016) Sergio Decherchi et al.   Communications in Computational Physics

A GPU-accelerated direct-sum boundary integral Poisson–Boltzmann solver

(2013) Weihua Geng et al.   COMPUTER PHYSICS COMMUNICATIONS

A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers

(2013) Christopher D. Cooper et al.   COMPUTER PHYSICS COMMUNICATIONS

Comparison of treecodes for computing electrostatic potentials in charged particle systems with disjoint targets and sources

(2013) Henry A. Boateng et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

A treecode-accelerated boundary integral Poisson–Boltzmann solver for electrostatics of solvated biomolecules

(2013) Weihua Geng et al.   JOURNAL OF COMPUTATIONAL PHYSICS

A general and Robust Ray-Casting-Based Algorithm for Triangulating Surfaces at the Nanoscale

(2013) Sergio Decherchi et al.   PLoS One

A Fast and Robust Poisson–Boltzmann Solver Based on Adaptive Cartesian Grids

(2011) Alexander H. Boschitsch et al.   Journal of Chemical Theory and Computation

TMSmesh: A Robust Method for Molecular Surface Mesh Generation Using a Trace Technique

(2010) Minxin Chen et al.   Journal of Chemical Theory and Computation

Assessment of linear finite-difference Poisson–Boltzmann solvers

(2010) Jun Wang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Multiscale molecular dynamics using the matched interface and boundary method

(2010) Weihua Geng et al.   JOURNAL OF COMPUTATIONAL PHYSICS

A Cartesian treecode for screened coulomb interactions

(2009) Peijun Li et al.   JOURNAL OF COMPUTATIONAL PHYSICS