PBSA implementation

[dprada]

Although Poisson-Boltzmann is not our priority, we have to start thinking how this implementation should be. Let's use this issue to collect some ideas.

There is a widely used tool to solve the Poisson-Boltzmann equation of continuum electrostatics, its the APBS (Adaptive Poisson-Boltzmann Solver). Many tools depend on this APBS implementation (maybe amber does it as well). Although there is a registration process to use it, it is embedded in some other packages (how? who knows...). We should look for python libraries using this tool.

Here the paper of the last version.

APBS repo in GitHub APBS documentation

PDB2PQR repo in GitHub # required to work with APBS PDB2PQR documentation

[dprada]

There is a list of software using APBS in the same APBS documentation.

[dprada]

APBS is shared under an MIT License. 👍🏻

[dprada]

If we finally include ABPS and PDB2QPR in BiFrEE, we should probably add in the main README a note similar to what is found in the PyMOL APBS plugin documentation:

---

APBS When using the APBS, you are "obligated" to register your use of the software. This will the authors able to require funding for further development. Register here, it takes 1 minutes: http://www.poissonboltzmann.org/apbs/downloads

Please acknowledge your use of APBS by citing: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. doi:10.1073/pnas.181342398

Please acknowledge your use of the Holst group software by citing: M. Holst and F. Saied, Multigrid solution of the Poisson-Boltzmann equation. J. Comput. Chem. 14, 105-113, 1993. M. Holst and F. Saied, Numerical solution of the nonlinear Poisson-Boltzmann equation: Developing more robust and efficient methods. J. Comput. Chem. 16, 337-364, 1995. For PMG (the multigrid solver): M. Holst, Adaptive numerical treatment of elliptic systems on manifolds. Advances in Computational Mathematics 15, 139-191, 2001. doi:10.1023/A:1014246117321 For FEtk (the finite element solver): R. Bank and M. Holst, A New Paradigm for Parallel Adaptive Meshing Algorithms. SIAM Review 45, 291-323, 2003. doi:10.1137/S003614450342061

pdb2pqr When using the pdb2pqr, you are "strongly encourage" to register your use of the software. This will the authors able to require funding for further development. Register here, it takes 1 minutes: http://www.poissonboltzmann.org/pdb2pqr/d/downloads

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[dprada]

There are some other tools we should check (we could also implement more than one to give the user the possibility to choose the PB solver). We have to have a look to PyGBe also!

PyGBe repo in GitHub

Papers: Cooper, C.D, Bardhan, J.P. and Barba, L.A. (2014), "A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers," Computer Physics Communications, 185(3): 720–729, doi: 10.1016/j.cpc.2013.10.028, arxiv:1309.4018 Cooper, C.D and Barba, L.A. (2016), "Poisson–Boltzmann model for protein–surface electrostatic interactions and grid-convergence study using the PyGBe code," Computer Physics Communications, 202: 23–32, doi: 10.1016/j.cpc.2015.12.019, arXiv:1506.03745 Cooper, C.D, Clementi, N.C. and Barba, L.A. (2015), "Probing protein orientation near charged nanosurfaces for simulation-assisted biosensor design," Journal of Chemical Physics, 143: 124709 doi: 10.1063/1.4931113, arXiv:1503.08150v4.

[dprada]

The main README file of the PyGBe repo includes a list of other alternative tools (we should also check):

https://github.com/pygbe/pygbe#other-software

There we can find volumetric-based solvers as Delphi and APBS, and boundary-element methods as AFMPB serial, AFMPB and TABI.

[dprada]

Let's have a look also to g_mmpbsa. It uses APBS.