Defining, Computing, and Visualizing Molecular Interfaces

Authors:
Amitabh Varshney;Frederick P. Brooks Jr;Dinesh Manocha;William V. Wright;David C. Richardson
Affiliations:
Department of Computer Science, State University of New York at Stony Brook, Stony Brook, NY;Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC;Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC;Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC;Department of Biochemistry, Duke University Medical Center, Durham, NC
Venue:
VIS '95 Proceedings of the 6th conference on Visualization '95
Year:
1995

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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 alpha and beta, where alpha is the radius of the solvent molecule (also known as the probe-radius) and beta 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(n k \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 alpha and beta.