APBS

APBS is a software package for the numerical 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. (Source: http://freecode.com/)


References in zbMATH (referenced in 88 articles )

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  1. Benner, Peter; Khoromskaia, Venera; Khoromskij, Boris; Kweyu, Cleophas; Stein, Matthias: Regularization of Poisson-Boltzmann-type equations with singular source terms using the range-separated tensor format (2021)
  2. Torsu, Prosper: On variational iterative methods for semilinear problems (2020)
  3. Zhao, Rundong; Wang, Menglun; Chen, Jiahui; Tong, Yiying; Wei, Guo-Wei: The de Rham-Hodge analysis and modeling of biomolecules (2020)
  4. Hazra, Tania; Ullah, Sheik Ahmed; Wang, Siwen; Alexov, Emil; Zhao, Shan: A super-Gaussian Poisson-Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states (2019)
  5. Lei, Huan; Li, Jing; Gao, Peiyuan; Stinis, Panagiotis; Baker, Nathan A.: A data-driven framework for sparsity-enhanced surrogates with arbitrary mutually dependent randomness (2019)
  6. Loisel, Sébastien; Nguyen, Hieu: On the convergence of an optimal additive Schwarz method for parallel adaptive finite elements (2019)
  7. Quan, Chaoyu; Stamm, Benjamin; Maday, Yvon: A domain decomposition method for the Poisson-Boltzmann solvation models (2019)
  8. Chaudhry, Jehanzeb H.: A posteriori analysis and efficient refinement strategies for the Poisson-Boltzmann equation (2018)
  9. Chen, Jiahui; Geng, Weihua: On preconditioning the treecode-accelerated boundary integral (TABI) Poisson-Boltzmann solver (2018)
  10. Egan, Raphael; Gibou, Frédéric: Fast and scalable algorithms for constructing solvent-excluded surfaces of large biomolecules (2018)
  11. Quan, Chaoyu; Stamm, Benjamin; Maday, Yvon: A domain decomposition method for the polarizable continuum model based on the solvent excluded surface (2018)
  12. Ying, Jinyong; Xie, Dexuan: A hybrid solver of size modified Poisson-Boltzmann equation by domain decomposition, finite element, and finite difference (2018)
  13. Zhong, Yimin; Ren, Kui; Tsai, Richard: An implicit boundary integral method for computing electric potential of macromolecules in solvent (2018)
  14. Chen, Duan: Fractional Poisson-Nernst-Planck model for ion channels. I: Basic formulations and algorithms (2017)
  15. Geng, Weihua; Zhao, Shan: A two-component matched interface and boundary (MIB) regularization for charge singularity in implicit solvation (2017)
  16. Loisel, Sébastien; Nguyen, Hieu: An optimal Schwarz preconditioner for a class of parallel adaptive finite elements (2017)
  17. Geng, Weihua: A boundary integral Poisson-Boltzmann solvers package for solvated bimolecular simulations (2015)
  18. Jiang, Yi; Xie, Yang; Ying, Jinyong; Xie, Dexuan; Yu, Zeyun: SDPBS web server for calculation of electrostatics of ionic solvated biomolecules (2015)
  19. Li, Bo; Sun, Hui; Zhou, Shenggao: Stability of a cylindrical solute-solvent interface: effect of geometry, electrostatics, and hydrodynamics (2015)
  20. Xie, Dexuan; Li, Jiao: A new analysis of electrostatic free energy minimization and Poisson-Boltzmann equation for protein in ionic solvent (2015)

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