Journal
JOURNAL OF COMPUTATIONAL CHEMISTRY
Volume 38, Issue 15, Pages 1275-1282Publisher
WILEY
DOI: 10.1002/jcc.24528
Keywords
electrostatics; Brownian dynamics; linearized Poisson-Boltzmann equation
Categories
Funding
- Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy [DE-AC02-05CH11231]
- National Science Foundation [DGE 110640]
- National Biomedical Computation Resource (APBS)
- National Institutes of Health [GM069702, 9P41GM104601, 5R01GM098243-02]
- National Energy Research Scientific Computing Center, a DOE Office of Science User Facility Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231]
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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. (c) 2016 Wiley Periodicals, Inc.
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