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 73 articles )

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  1. Zhong, Yimin; Ren, Kui; Tsai, Richard: An implicit boundary integral method for computing electric potential of macromolecules in solvent (2018)
  2. Chen, Duan: Fractional Poisson-Nernst-Planck model for ion channels. I: Basic formulations and algorithms (2017)
  3. Geng, Weihua; Zhao, Shan: A two-component matched interface and boundary (MIB) regularization for charge singularity in implicit solvation (2017)
  4. Loisel, Sébastien; Nguyen, Hieu: An optimal Schwarz preconditioner for a class of parallel adaptive finite elements (2017)
  5. Geng, Weihua: A boundary integral Poisson-Boltzmann solvers package for solvated bimolecular simulations (2015)
  6. Jiang, Yi; Xie, Yang; Ying, Jinyong; Xie, Dexuan; Yu, Zeyun: SDPBS web server for calculation of electrostatics of ionic solvated biomolecules (2015)
  7. Li, Bo; Sun, Hui; Zhou, Shenggao: Stability of a cylindrical solute-solvent interface: effect of geometry, electrostatics, and hydrodynamics (2015)
  8. Xie, Dexuan; Li, Jiao: A new analysis of electrostatic free energy minimization and Poisson-Boltzmann equation for protein in ionic solvent (2015)
  9. Ying, Jinyong; Xie, Dexuan: A new finite element and finite difference hybrid method for computing electrostatics of ionic solvated biomolecule (2015)
  10. 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)
  11. Chen, Duan: Modeling and computation of heterogeneous implicit solvent and its applications for biomolecules (2014)
  12. 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)
  13. Jiang, Yi; Ying, Jinyong; Xie, Dexuan: A Poisson-Boltzmann equation test model for protein in spherical solute region and its applications (2014)
  14. Xia, Kelin; Feng, Xin; Chen, Zhan; Tong, Yiying; Wei, Guo-Wei: Multiscale geometric modeling of macromolecules. I: Cartesian representation (2014)
  15. Xie, Dexuan: New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics (2014)
  16. Geng, Weihua: Parallel higher-order boundary integral electrostatics computation on molecular surfaces with curved triangulation (2013)
  17. Geng, Weihua; Jacob, Ferosh: A GPU-accelerated direct-sum boundary integral Poisson-Boltzmann solver (2013)
  18. Geng, Weihua; Krasny, Robert: A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules (2013)
  19. Geng, Weihua; Zhao, Shan: Fully implicit ADI schemes for solving the nonlinear Poisson-Boltzmann equation (2013)
  20. Harris, Robert C.; Mackoy, Travis; Fenley, Marcia O.: A stochastic solver of the generalized Born model (2013)

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