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J Comput Chem. 2017 Jun 5;38(15):1275-1282. doi: 10.1002/jcc.24528. Epub 2016 Nov 2.

PB-AM: An open-source, fully analytical linear poisson-boltzmann solver.

Author information

1
Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California, 94720.
2
Department of Chemistry, University of California Berkeley, Berkeley, California, 94720.
3
Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, 10461.
4
Division of Computational and Statistical Analytics, Pacific Northwest National Laboratory, Richland, Washington, 99352.
5
Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, Utah, 84112.
6
Advanced Computing, Mathematics, and Data Division, Pacific Northwest National Laboratory, Richland, Washington, 99352.
7
Division of Applied Mathematics, Brown University, Providence, Rhode Island, 02912.
8
Department of Bioengineering, University of California Berkeley, Berkeley, California, 94720.
9
Chemical Sciences Division, Lawrence Berkeley National Labs, Berkeley, California, 94720.

Abstract

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.

KEYWORDS:

Brownian dynamics; electrostatics; linearized Poisson-Boltzmann equation

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