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by Amitabh Varshney, Frederick P. Brooks, David C. Richardson, William V. Wright, Dinesh Manocha
ftp://ftp.cs.sunysb.edu/pub/virtual/varshney/molecular_interface.ps.gz
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Abstract:
A parallel, analytic approach for defining and computing the inter- and intra-molecular interfaces in three dimensions is described. The molecular interface surfaces are derived from approximations to the power-diagrams over the participating molecular units. For a given molecular interface our approach can generate a family of interface surfaces parametrized by ff and fi, where ff is the radius of the solvent molecule (also known as the probe-radius) and fi is the interface radius that defines the size of the molecular interface. Molecular interface surfaces provide biochemists with a powerful tool to study surface complementarity and to efficiently characterize the interactions during a protein-substrate docking. The complexity of our algorithm for molecular environments is O(nk log 2 k), where n is the number of atoms in the participating molecular units and k is the average number of neighboring atoms-- a constant, given ff and fi. 1
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