PB-AM: An Open-Source, Fully Analytical Linear Poisson-Boltzmann Solver

TL;DR

PB-AM is an open-source, fully analytical solver for the linearized Poisson-Boltzmann equation, enabling detailed biomolecular electrostatics analysis and dynamics simulation with visualization and docking features.

Contribution

It introduces a fully analytical, open-source solver for the linearized Poisson-Boltzmann equation with integrated dynamics, docking, and visualization capabilities, and enhances accessibility via integration with APBS.

Findings

Provides accurate mutual polarization modeling

Supports biomolecular dynamics with periodic boundary conditions

Facilitates biomolecular docking and association rate calculations

Abstract

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 molecules represented as non-overlapping spherical cavities. The PB-AM software package includes the generation of outputs files appropriate for visualization using VMD, a Brownian dynamics scheme that uses periodic boundary conditions to simulate dynamics, the ability to specify docking criteria, and offers two different kinetics schemes to evaluate biomolecular association rate constants. Given that PB-AM defines mutual polarization completely and accurately, it can be refactored as a many-body expansion to explore 2- and 3-body polarization. Additionally, the software has been integrated into the Adaptive Poisson-Boltzmann Solver (APBS) software package to make it more accessible to a larger group of scientists, educators and students that are more familiar with the APBS framework.