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Research methodologies used

  • Molecular dynamics simulation (GROMOS and GROMACS packages)
      • Free-energy perturbation methods
  • Continuum electrostatics
      • Monte-Carlo titration in the framework of continuum electrostatics methods (MCRP and PETIT)
      • Electrostatic pKa and redox potential calculations (MEAD)
      • Poisson-Boltzmann Surface Area
  • Comparative modelling methods (MODELLER)
  • Electron transfer pathways calculations (GREENPATH)
  • Protein-protein interactions (AUTODOCK combined with molecular dynamics simulations)
  • Molecular graphics
  • Our own in house software for several modelling methods


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