The volume of atoms on the protein surface: calculated from simulation, using Voronoi polyhedra.

  title={The volume of atoms on the protein surface: calculated from simulation, using Voronoi polyhedra.},
  author={Mark B. Gerstein and Jerry Tsai and Michael Levitt},
  journal={Journal of molecular biology},
  volume={249 5},
We analyze the volume of atoms on the protein surface during a molecular-dynamics simulation of a small protein (pancreatic trypsin inhibitor). To calculate volumes, we use a particular geometric construction, called Voronoi polyhedra, that divides the total volume of the simulation box amongst the atoms, rendering them relatively larger or smaller depending on how tightly they are packed. We find that most of the atoms on the protein surface are larger than those buried in the core (by… 

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