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APBS

Adaptive Poisson-Boltzmann Solver (APBS) -- Software for evaluating the electrostatic properties of nanoscale biomolecular systems

APBS is a software package for modeling biomolecular solvation through solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including:
  • simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics,
  • implicit solvent molecular dynamics of biomolecules,
  • solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design,
  • and biomolecular titration studies.
APBS was designed to efficiently evaluate electrostatic properties for such simulations for a wide range of length scales to enable the investigation of molecules with tens to millions of atoms. We also provide implicit solvent models of nonpolar solvation which accurately account for both repulsive and attractive solute-solvent interactions.

This software was written by Nathan Baker in collaboration with J. Andrew McCammon and Michael Holst. APBS has been enhanced by contributions from several other authors.

APBS uses FEtk (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FEtk is a portable collection of finite element modeling class libraries written in an object-oriented version of C. It is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at http://www.FEtk.org.

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