Defining, Computing, and Visualizing Molecular Interfaces

TitleDefining, Computing, and Visualizing Molecular Interfaces
Publication TypeConference Papers
Year of Publication1995
AuthorsVarshney A, Brooks Jr FP, Manocha D, Wright WV, Richardson DC
Conference NameProceedings of the 6th conference on Visualization '95
Date Published1995///
PublisherIEEE Computer Society
Conference LocationWashington, DC, USA
ISBN Number0-8186-7187-4
KeywordsComputational Biochemistry Algorithms Molecular Graphics, Connolly Surfaces, Molecular Interfaces, Molecular Surfaces, Protein-Protein Recognition

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.