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

Lisa E Felberg1, David H Brookes2, Eng-Hui Yap3

  • 1Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California, 94720.

Journal of Computational Chemistry
|November 3, 2016
PubMed
Summary
This summary is machine-generated.

We introduce the Poisson-Boltzmann Analytical Method (PB-AM) software for accurate molecular modeling. This open-source tool provides analytical solutions for biomolecular interactions and kinetics, enhancing scientific research accessibility.

Keywords:
Brownian dynamicselectrostaticslinearized Poisson-Boltzmann equation

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Area of Science:

  • Computational chemistry
  • Biophysics
  • Molecular modeling

Background:

  • The Poisson-Boltzmann equation is crucial for understanding electrostatic interactions in biological systems.
  • Existing methods often involve numerical approximations, limiting accuracy and speed.
  • Accurate calculation of biomolecular association rates is essential for drug discovery and understanding biological processes.

Purpose of the Study:

  • To present the open-source distributed software package Poisson-Boltzmann Analytical Method (PB-AM).
  • To provide a fully analytical solution to the linearized Poisson-Boltzmann equation for molecular systems.
  • To enhance the evaluation of biomolecular association rate constants and explore molecular polarization.

Main Methods:

  • Developed a fully analytical solution to the linearized Poisson-Boltzmann equation for non-overlapping spherical cavities.
  • Implemented features for generating visualization files, Brownian dynamics simulations with periodic boundary conditions, and docking criteria specification.
  • Incorporated two distinct kinetics schemes for calculating biomolecular association rate constants.
  • Refactored the method as a many-body expansion to analyze 2- and 3-body polarization effects.
  • Integrated PB-AM into the Adaptive Poisson-Boltzmann Solver (APBS) framework.

Main Results:

  • PB-AM offers a complete and accurate definition of mutual polarization.
  • The software facilitates the exploration of 2- and 3-body polarization effects.
  • Integration with APBS increases accessibility for a broader scientific community.
  • The package supports molecular visualization and Brownian dynamics simulations.

Conclusions:

  • PB-AM provides a powerful, open-source tool for accurate electrostatic calculations in molecular modeling.
  • The analytical approach and integration with APBS significantly advance the study of biomolecular interactions and kinetics.
  • This software empowers scientists, educators, and students with enhanced capabilities for molecular simulations and analysis.