PB-AM: An open-source, fully analytical linear poisson-boltzmann solver.
We present the open source distributed software package Poisson-Boltzmann Analytical Method (PB-AM), a fully analytical solution to the linearized PB equation, for molecules represented as non-overlapping spherical cavities. The PB-AM software package includes the generation of outputs files appropriate for visualization using visual molecular dynamics, 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. © 2016 Wiley Periodicals, Inc.
['Felberg|Lisa E|LE|', 'Brookes|David H|DH|', 'Yap|Eng-Hui|EH|', 'Jurrus|Elizabeth|E|', 'Baker|Nathan A|NA|', 'Head-Gordon|Teresa|T|']
D000465:Algorithms D007700:Kinetics D056004:Molecular Dynamics Simulation D011506:Proteins D012984:Software D055672:Static Electricity
Brownian dynamics electrostatics linearized Poisson-Boltzmann equation