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Author Ban, Yih-En Andrew ♦ Edelsbrunner, Herbert ♦ Rudolph, Johannes
Source ACM Digital Library
Content type Text
Publisher Association for Computing Machinery (ACM)
File Format PDF
Copyright Year ©2006
Language English
Subject Domain (in DDC) Computer science, information & general works ♦ Data processing & computer science
Subject Keyword Filtrations ♦ Voronoi diagrams ♦ Geometric and topological algorithms ♦ Interface surfaces ♦ Protein interaction
Abstract Protein-protein interactions, which form the basis for most cellular processes, result in the formation of protein interfaces. Believing that the local shape of proteins is crucial, we take a geometric approach and present a definition of an interface surface formed by two or more proteins as a subset of their Voronoi diagram. The definition deals with the difficult and important problem of specifying interface boundaries by invoking methods used in the alpha shape representation of molecules, the discrete flow on Delaunay simplices to define pockets and reconstruct surfaces, and the assessment of the importance of topological features. We present an algorithm to construct the surface and define a hierarchy that distinguishes core and peripheral regions. This hierarchy is shown to have correlation with hot-spots in protein-protein interactions. Finally, we study the geometric and topological properties of interface surfaces and show their high degree of contortion.
ISSN 00045411
Age Range 18 to 22 years ♦ above 22 year
Educational Use Research
Education Level UG and PG
Learning Resource Type Article
Publisher Date 2006-05-01
Publisher Place New York
e-ISSN 1557735X
Journal Journal of the ACM (JACM)
Volume Number 53
Issue Number 3
Page Count 18
Starting Page 361
Ending Page 378


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Source: ACM Digital Library