External Contributions

The following is a brief summary of some external contributions that have been added to APBS. Click on the links to learn more about each contribution and its usage in APBS.

PB-AM: Poisson-Boltzmann Analytical method

The Poisson-Boltzmann Analytical method was developed in 2006 by Lotan, Head-Gordon (2006). It has been implemented into APBS by Felberg, Brookes and Head-Gordon.

Barnase/Barstar system isosurfaces created in PB-AM.

By coarse-graining each molecule in the system into a sphere, the analytical model is able to solve the linearized Poisson-Boltzmann efficiently and accurately.

For more details, please visit the APBS PB-AM documentation.

PB-SAM: Poisson-Boltzmann Semi-Analytical method

The Poisson-Boltzmann Semi-Analytical method was developed in 2010 by Yap, Head-Gordon (2010). It has been implemented into APBS by Felberg, Brookes and Head-Gordon.

Barnase/Barstar system isosurfaces created in PB-SAM.

By coarse-graining each molecule in the system into many overlapping spheres, the semi-analytical model expands on the formalism of the analytical method and is able to solve the linearized Poisson-Boltzmann efficiently and accurately.

For more details, please visit the APBS PB-SAM documentation.

TABI-PB: Treecode-Accelerated Boundary Integral Poisson-Boltzmann method

The Treecode-Accelerated Boundary Integral Poisson-Boltzmann method (TABI-PB) was developed by Geng, Krasny (2013). It has been implemented into APBS by Chen and Wilson.

It is implicit Poisson-Boltzmann solver based on well-conditioned boundary integral equations, and with treecode algorithm reduced the computational costs from O(N^2) to O(NlogN). TABI-PB gives solvation energy, surface potential, and the triangularization generated by MSMS or NanoShaper.

For more details, please visit the APBS TABI documentation.

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