Further reading

General solvation reviews

APBS parallel solvers

  • 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, 10037-41, 2001. http://dx.doi.org/10.1073/pnas.181342398

  • Baker NA, Sept D, Holst MJ, McCammon JA. The adaptive multilevel finite element solution of the Poisson-Boltzmann equation on massively parallel computers. IBM J Res Devel, 45, 427-38, 2001. http://dx.doi.org/10.1147/rd.453.0427

APBS multigrid solver

    1. Holst, Adaptive numerical treatment of elliptic systems on manifolds. Advances in Computational Mathematics 15, 139-191, 2001 http://dx.doi.org/10.1023/A:1014246117321

    1. 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.

    1. Holst and F. Saied, Multigrid solution of the Poisson-Boltzmann equation. J. Comput. Chem. 14, 105-113, 1993.

APBS finite element solver

  • Holst M, Baker NA, Wang F. Adaptive multilevel finite element solution of the Poisson-Boltzmann equation I: algorithms and examples. J Comput Chem, 21, 1319-42, 2000. http://bit.ly/1goFAFE

  • Baker N, Holst M, Wang F. Adaptive multilevel finite element solution of the Poisson-Boltzmann equation II: refinement schemes based on solvent accessible surfaces. J Comput Chem, 21, 1343-52, 2000. http://bit.ly/1dNSP8l

APBS geometric flow solver

  • Chen Z, Baker NA, Wei GW. Differential geometry based solvation model I: Eulerian formulation, J Comput Phys, 229, 8231-58, 2010. http://dx.doi.org/10.1016/j.jcp.2010.06.036

  • Chen Z, Baker NA, Wei GW. Differential geometry based solvation model II: Lagrangian formulation. J Math Biol, 63, 1139-1200, 2011. http://dx.doi.org/10.1007/s00285-011-0402-z

  • Chen Z, Zhao S, Chun J, Thomas DG, Baker NA, Wei GW. Variational approach for nonpolar solvation analysis. Journal of Chemical Physics, 137, 084101, 2012. http://dx.doi.org/10.1063/1.4745084

  • Thomas DG, Chun J, Chen Z, Wei G, Baker NA. Parameterization of a Geometric flow implicit solvation model. Journal of Computational Chemistry, 34, 687-95, 2013. http://dx.doi.org/10.1002/jcc.23181

  • Daily M, Chun J, Heredia-Langner A, Baker NA. Origin of parameter degeneracy and molecular shape relationships in geometric-flow calculations of solvation free energies. J Chem Phys, 139, 204108, 2013. http://dx.doi.org/10.1063/1.4832900

TABI-PB boundary element solver

  • Geng W, Krasny R. A treecode-accelerated boundary integral Poisson–Boltzmann solver for electrostatics of solvated biomolecules, J Comput Phys, 247, 62-78, 2013. https://doi.org/10.1016/j.jcp.2013.03.056

Structural bioinformatics based on electrostatic properties

  • Zhang X, Bajaj CL, Kwon B, Dolinsky TJ, Nielsen JE, Baker NA. Application of new multi-resolution methods for the comparison of biomolecular electrostatic properties in the absence of global structural similarity. Multiscale Model Simul, 5, 1196-213, 2006. http://dx.doi.org/10.1137/050647670

  • Chakraborty S, Rao BJ, Baker N, Ásgeirsson B. Structural phylogeny by profile extraction and multiple superimposition using electrostatic congruence as a discriminator. Intrinsically Disordered Proteins, 1 (1), e25463, 2013. https://www.landesbioscience.com/journals/idp/article/25463/

Other fun with APBS

  • Wagoner JA, Baker NA. Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms. Proc Natl Acad Sci USA, 103, 8331-6, 2006. http://dx.doi.org/10.1073/pnas.0600118103

  • Swanson JMJ, Wagoner JA, Baker NA, McCammon JA. Optimizing the Poisson dielectric boundary with explicit solvent forces and energies: lessons learned with atom-centered dielectric functions. J Chem Theory Comput, 3, 170-83, 2007. http://dx.doi.org/10.1021/ct600216k

  • Schnieders MJ, Baker NA, Ren P, Ponder JW. Polarizable Atomic Multipole Solutes in a Poisson-Boltzmann Continuum. J Chem Phys, 126, 124114, 2007. http://dx.doi.org/10.1063/1.2714528

  • Callenberg KM, Choudhary OP, de Forest GL, Gohara DW, Baker NA, Grabe M. APBSmem: A graphical interface for electrostatic calculations at the membrane. PLoS ONE, 5, e12722, 2010. http://dx.doi.org/10.1371/journal.pone.0012722

  • Unni S, Huang Y, Hanson RM, Tobias M, Krishnan S, Li WW, Nielsen JE, Baker NA. Web servers and services for electrostatics calculations with APBS and PDB2PQR. J Comput Chem, 32 (7), 1488-1491, 2011. http://dx.doi.org/10.1002/jcc.21720

  • Konecny R, Baker NA, McCammon JA. iAPBS: a programming interface to the adaptive Poisson–Boltzmann solver. Computational Science and Discovery, 5, 015005, 2012. http://dx.doi.org/10.1088/1749-4699/5/1/015005

  • Jurrus E, Engel D, Star K, Monson K, Brandi J, Felberg LE, Brookes DH, Wilson L, Chen J, Liles K, Chun M, Li P, Gohara DW, Dolinsky T, Konecny R, Koes DR, Nielsen JE, Head-Gordon T, Geng W, Krasny R, Wei G-W, Holst MJ, McCammon JA, Baker NA. Improvements to the APBS biomolecular solvation software suite. Protein Sci, 27 (1), 112-128, 2018. https://doi.org/10.1002/pro.3280

  • Laureanti J, Brandi J, Offor E, Engel D, Rallo R, Ginovska B, Martinez X, Baaden M, Baker NA. Visualizing biomolecular electrostatics in virtual reality with UnityMol‐APBS. Protein Sci, 29 (1), 237-246, 2020. https://doi.org/10.1002/pro.3773