Memetic algorithms for ligand expulsion from protein cavities.

  title={Memetic algorithms for ligand expulsion from protein cavities.},
  author={Jakub Rydzewski and Wiesław Nowak},
  journal={The Journal of chemical physics},
  volume={143 12},
Ligand diffusion through a protein interior is a fundamental process governing biological signaling and enzymatic catalysis. A complex topology of channels in proteins leads often to difficulties in modeling ligand escape pathways by classical molecular dynamics simulations. In this paper, two novel memetic methods for searching the exit paths and cavity space exploration are proposed: Memory Enhanced Random Acceleration (MERA) Molecular Dynamics (MD) and Immune Algorithm (IA). In MERA, a… 

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