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A general algorithm for computing Voronoi volumes: Application to the hydrated crystal of myoglobin
Author(s) -
Procacci Piero,
Scateni Riccardo
Publication year - 1992
Publication title -
international journal of quantum chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.484
H-Index - 105
eISSN - 1097-461X
pISSN - 0020-7608
DOI - 10.1002/qua.560420525
Subject(s) - myoglobin , voronoi diagram , degenerate energy levels , polyhedron , diffraction , crystallography , volume (thermodynamics) , crystal (programming language) , square (algebra) , chemistry , materials science , algorithm , mathematics , physics , thermodynamics , combinatorics , computer science , geometry , quantum mechanics , organic chemistry , programming language
In this study is presented a general algorithm for computing Voronoi volumes of atoms of group of atoms in condensed phases. The method is essentially an extension of the Medvedev procedure to allow vertice determination for any Voronoi polyhedron, primitive or with degenerate vertices. The algorithm has been employed for computing time‐averaged volumes in the hydrated crystal of met‐myoglobin, using the data of a molecular dynamics simulation. The results, compared to previous volume determination in myoglobin, emphasize the fundamental role of solvent structure close to the protein surface in relation to the packing density properties of the residues. Relative volumes fluctuations of myoglobin residues have been found to be correlated to the corresponding mean square displacements from X‐ray diffraction studies and to the theoretical hydration energies.