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 65 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. Ying, Jinyong; Xie, Dexuan: A new finite element and finite difference hybrid method for computing electrostatics of ionic solvated biomolecule (2015)
  5. 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)
  6. Chen, Duan: Modeling and computation of heterogeneous implicit solvent and its applications for biomolecules (2014)
  7. Cooper, Christopher D.; Bardhan, Jaydeep P.; Barba, L.A.: A biomolecular electrostatics solver using python, GPUs and boundary elements that can handle solvent-filled cavities and stern layers (2014)
  8. Jiang, Yi; Ying, Jinyong; Xie, Dexuan: A Poisson-Boltzmann equation test model for protein in spherical solute region and its applications (2014)
  9. Xia, Kelin; Feng, Xin; Chen, Zhan; Tong, Yiying; Wei, Guo-Wei: Multiscale geometric modeling of macromolecules. I: Cartesian representation (2014)
  10. Xie, Dexuan: New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics (2014)
  11. Geng, Weihua: Parallel higher-order boundary integral electrostatics computation on molecular surfaces with curved triangulation (2013)
  12. Geng, Weihua; Jacob, Ferosh: A GPU-accelerated direct-sum boundary integral Poisson-Boltzmann solver (2013)
  13. Geng, Weihua; Krasny, Robert: A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules (2013)
  14. Aksoylu, Burak; Bond, Stephen D.; Cyr, Eric C.; Holst, Michael: Goal-oriented adaptivity and multilevel preconditioning for the Poisson-Boltzmann equation (2012)
  15. Chaudhry, Jehanzeb Hameed; Bond, Stephen D.; Olson, Luke N.: A weighted adaptive least-squares finite element method for the Poisson-Boltzmann equation (2012)
  16. Bajaj, Chandrajit; Chen, Shun-Chuan; Rand, Alexander: An efficient higher-order fast multipole boundary element solution for Poisson-Boltzmann-based molecular electrostatics (2011)
  17. Chaudhry, Jehanzeb Hameed; Bond, Stephen D.; Olson, Luke N.: Finite element approximation to a finite-size modified Poisson-Boltzmann equation (2011)
  18. Fennell, Christopher J.; Dill, Ken A.: Physical modeling of aqueous solvation (2011)
  19. Geng, Weihua; Wei, G.W.: Multiscale molecular dynamics using the matched interface and boundary method (2011)
  20. Helgadóttir, Ásdís; Gibou, Frédéric: A Poisson-Boltzmann solver on irregular domains with Neumann or Robin boundary conditions on non-graded adaptive grid (2011)

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