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

Felberg, Lisa E.; Brookes, David H.; Yap, Eng-Hui; Jurrus, Elizabeth; Baker, Nathan A.; Head-Gordon, Teresa

doi:10.1002/jcc.24528

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

Journal Article · Wed Nov 02 00:00:00 EDT 2016 · Journal of Computational Chemistry

DOI:https://doi.org/10.1002/jcc.24528· OSTI ID:1361960

Felberg, Lisa E. ^[1]; Brookes, David H. ^[2]; Yap, Eng-Hui ^[3]; Jurrus, Elizabeth ^[4]; Baker, Nathan A. ^[5]; Head-Gordon, Teresa ^[6]

Univ. of California, Berkeley, CA (United States). Dept. of Chemical and Biomolecular Engineering
Univ. of California, Berkeley, CA (United States). Dept. of Chemistry
Albert Einstein College of Medicine, Bronx, NY (United States). Dept. of Systems and Computational Biology
Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Division of Computational and Statistical Analytics; Univ. of Utah, Salt Lake City, UT (United States). Scientific Computing and Imaging (SCI) Inst.
Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Advanced Computing, Mathematics, and Data Division; Brown Univ., Providence, RI (United States). Division of Applied Mathematics
Univ. of California, Berkeley, CA (United States). Dept. of Chemical and Biomolecular Engineering and Dept. of Chemistry and Dept. of Bioengineering; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Chemical Sciences Division

We present the open source distributed software package Poisson-Boltzmann Analytical Method (PB-AM), a fully analytical solution to the linearized Poisson Boltzmann equation. 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.

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22). Scientific User Facilities Division; National Science Foundation (NSF); National Inst. of Health (NIH); National Biomedical Computation Resource

DOE Contract Number:: AC05-76RL01830; AC02-05CH11231

OSTI ID:: 1361960

Report Number(s):: PNNL-SA--120107; 453040220

Journal Information:: Journal of Computational Chemistry, Journal Name: Journal of Computational Chemistry Journal Issue: 15 Vol. 38; ISSN 0192-8651

Publisher:: Wiley

Country of Publication:: United States

Language:: English

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Improvements to the APBS biomolecular solvation software suite Jurrus, Elizabeth; Engel, Dave; Star, Keith arXiv https://doi.org/10.48550/arxiv.1707.00027	text	January 2017
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