Simplicial neighborhood analysis of protein packing (SNAPP): a computational geometry approach to studying proteins.

Publisher Summary This chapter describes the application of computational geometry methodology to protein-structure analysis and comparison. The Simplicial Neighborhood Analysis of Protein Packing (SNAPP) method is applied to the problem of automatically identifying recurrent substructures in a large database of diverse protein structures. The chapter presents a novel approach to mapping protein cores with application to fold recognition via structural templates. It also describes the use of the SNAPP methodology for recognizing functional patterns characteristic of three unique protein families. SNAPP employs Delaunay tessellation to identify recurrent tertiary packing motifs that may be characteristic of protein structural and functional families. This method includes automatic identification of elementary tertiary packing motifs recurring in a large database of protein structures, automatic identification of global patterns of protein structure organization by recognizing the protein's hydrophobic core, and identification of functional signature motifs in a family of proteins that can assist structure-based annotation.

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