Three-dimensional alpha shapes
ACM Transactions on Graphics (TOG)
On the definition and the construction of pockets in macromolecules
Discrete Applied Mathematics - Special volume on computational molecular biology DAM-CMB series volume 2
Defining, Computing, and Visualizing Molecular Interfaces
VIS '95 Proceedings of the 6th conference on Visualization '95
Local and Global Comparison of Continuous Functions
VIS '04 Proceedings of the conference on Visualization '04
Geometry and Topology for Mesh Generation (Cambridge Monographs on Applied and Computational Mathematics)
On persistent homotopy, knotted complexes and the Alexander module
Proceedings of the 3rd Innovations in Theoretical Computer Science Conference
Segmenting motifs in protein-protein interface surfaces
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
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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.