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 56 articles )

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  1. Geng, Weihua: A boundary integral Poisson-Boltzmann solvers package for solvated bimolecular simulations (2015)
  2. Jiang, Yi; Xie, Yang; Ying, Jinyong; Xie, Dexuan; Yu, Zeyun: SDPBS web server for calculation of electrostatics of ionic solvated biomolecules (2015)
  3. Xie, Dexuan; Li, Jiao: A new analysis of electrostatic free energy minimization and Poisson-Boltzmann equation for protein in ionic solvent (2015)
  4. Zhang, Bo; Peng, Bo; Huang, Jingfang; Pitsianis, Nikos P.; Sun, Xiaobai; Lu, Benzhuo: Parallel AFMPB solver with automatic surface meshing for calculation of molecular solvation free energy (2015)
  5. Chen, Duan: Modeling and computation of heterogeneous implicit solvent and its applications for biomolecules (2014)
  6. Jiang, Yi; Ying, Jinyong; Xie, Dexuan: A Poisson-Boltzmann equation test model for protein in spherical solute region and its applications (2014)
  7. Geng, Weihua; Jacob, Ferosh: A GPU-accelerated direct-sum boundary integral Poisson-Boltzmann solver (2013)
  8. Aksoylu, Burak; Bond, Stephen D.; Cyr, Eric C.; Holst, Michael: Goal-oriented adaptivity and multilevel preconditioning for the Poisson-Boltzmann equation (2012)
  9. Chaudhry, Jehanzeb Hameed; Bond, Stephen D.; Olson, Luke N.: A weighted adaptive least-squares finite element method for the Poisson-Boltzmann equation (2012)
  10. Bajaj, Chandrajit; Chen, Shun-Chuan; Rand, Alexander: An efficient higher-order fast multipole boundary element solution for Poisson-Boltzmann-based molecular electrostatics (2011)
  11. Chaudhry, Jehanzeb Hameed; Bond, Stephen D.; Olson, Luke N.: Finite element approximation to a finite-size modified Poisson-Boltzmann equation (2011)
  12. Fennell, Christopher J.; Dill, Ken A.: Physical modeling of aqueous solvation (2011)
  13. Geng, Weihua; Wei, G.W.: Multiscale molecular dynamics using the matched interface and boundary method (2011)
  14. Helgadóttir, Ásdís; Gibou, Frédéric: A Poisson-Boltzmann solver on irregular domains with Neumann or Robin boundary conditions on non-graded adaptive grid (2011)
  15. Mirzadeh, Mohammad; Theillard, Maxime; Gibou, Frédéric: A second-order discretization of the nonlinear Poisson-Boltzmann equation over irregular geometries using non-graded adaptive Cartesian grids (2011)
  16. Xie, Dexuan; Scott, L.Ridgway: A new boundary integral equation for molecular electrostatics with charges over whole space (2011)
  17. Xu, Zhenli; Cai, Wei: Fast analytical methods for macroscopic electrostatic models in biomolecular simulations (2011)
  18. Yokota, Rio; Bardhan, Jaydeep P.; Knepley, Matthew G.; Barba, L.A.; Hamada, Tsuyoshi: Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUs and a billion unknowns (2011)
  19. Bajaj, Chandrajit; Zhao, Wenqi: Fast molecular solvation energetics and forces computation (2010)
  20. Bossy, Mireille; Champagnat, Nicolas; Maire, Sylvain; Talay, Denis: Probabilistic interpretation and random walk on spheres algorithms for the Poisson-Boltzmann equation in molecular dynamics (2010)

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