August 23, 2017 | Elizabeth Jurrus*, Dave Engel*, Keith Star*, Kyle Monson*, Juan Brandi*, Lisa E. Felberg†, David H. Brookes†, Leighton Wilson‡, Jiahui Chen§, Karina Liles*, Minju Chun*, Peter Li*, David W. Gohara°, Todd Dolinsky||, Robert Konecny∆, David R. Koes▷, Jens Erik Nielsen♣, Teresa Head-Gordon†, Weihua Geng§, Robert Krasny‡, Guo-Wei Wei∇, Michael J. Holst∆, J. Andrew McCammon∆, and Nathan A. Baker∆
The APBS software suite has been continuously updated since its release in 2001 to address new research applications and improve computational capabilities. This paper discusses recent improvements in APBS, including a Poisson-Boltzmann analytical and semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory-based algorithm for determining pKa values, and an improved web-based visualization tool for electrostatics. APBS is used for solving the Poisson-Boltzmann equation to evaluate electrostatic potentials and other solvation properties. The software includes PDB2PQR, which converts PDB files to PQR format for electrostatic calculations. PDB2PQR automatically sets up, executes, and optimizes the structure for Poisson-Boltzmann electrostatics calculations, outputting a PQR file that can be used with APBS or other modeling software. The software also includes several methods for determining pKa values, including empirical and implicit solvent methods. APBS supports a variety of solvers, including finite difference and finite element solvers, and boundary element methods. The software also includes analytical and semi-analytical methods for solving the Poisson-Boltzmann equation, such as PB-AM and PB-SAM. APBS is used for visualization, structural analysis, diffusion simulations, and other calculations that require global electrostatic properties. The software is also used for other applications, including post-simulation energetic analyses, understanding protein-nanoparticle interactions, nucleic acid-ion interactions, biomolecular docking, and ligand binding. APBS is integrated with other software packages and can be used for molecular simulation programs such as AMBER, CHARMM, NAMD, Rosetta, and TINKER. The software is also used for protein surface electrostatics analysis, simulation of protein-protein association kinetics through Brownian dynamics, and evaluation of biomolecular kinetics. APBS is designed with modern principles to ensure its ability to interface with other computational packages and evolve as methods and applications change over time. The software is based on an object-oriented programming paradigm with strict ANSI-C compliance, enabling long-term sustainability and extensibility. The future of APBS includes building infrastructure to enable users to implement their own models and methods, and to run on a common system. The software is supported by several grants and is used by a large community of users.The APBS software suite has been continuously updated since its release in 2001 to address new research applications and improve computational capabilities. This paper discusses recent improvements in APBS, including a Poisson-Boltzmann analytical and semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory-based algorithm for determining pKa values, and an improved web-based visualization tool for electrostatics. APBS is used for solving the Poisson-Boltzmann equation to evaluate electrostatic potentials and other solvation properties. The software includes PDB2PQR, which converts PDB files to PQR format for electrostatic calculations. PDB2PQR automatically sets up, executes, and optimizes the structure for Poisson-Boltzmann electrostatics calculations, outputting a PQR file that can be used with APBS or other modeling software. The software also includes several methods for determining pKa values, including empirical and implicit solvent methods. APBS supports a variety of solvers, including finite difference and finite element solvers, and boundary element methods. The software also includes analytical and semi-analytical methods for solving the Poisson-Boltzmann equation, such as PB-AM and PB-SAM. APBS is used for visualization, structural analysis, diffusion simulations, and other calculations that require global electrostatic properties. The software is also used for other applications, including post-simulation energetic analyses, understanding protein-nanoparticle interactions, nucleic acid-ion interactions, biomolecular docking, and ligand binding. APBS is integrated with other software packages and can be used for molecular simulation programs such as AMBER, CHARMM, NAMD, Rosetta, and TINKER. The software is also used for protein surface electrostatics analysis, simulation of protein-protein association kinetics through Brownian dynamics, and evaluation of biomolecular kinetics. APBS is designed with modern principles to ensure its ability to interface with other computational packages and evolve as methods and applications change over time. The software is based on an object-oriented programming paradigm with strict ANSI-C compliance, enabling long-term sustainability and extensibility. The future of APBS includes building infrastructure to enable users to implement their own models and methods, and to run on a common system. The software is supported by several grants and is used by a large community of users.