Comparing Graph Representations of Protein Structure for Mining Family-Specific Residue-Based Packing Motifs

• DOI: 10.1089/cmb.2005.12.657
• Publication Date: 2005-08-18T14:36:58Z
• Authors: Jun Huan; Deepak Bandyopadhyay; Wei Wang; Jack Snoeyink; Jan Prins; Alexander Tropsha
• Keywords: Models, Molecular; Models, Statistical; Molecular Structure; Amino Acid Motifs; Computational Biology; Proteins; 02 engineering and technology; Structural Homology, Protein; Computer Graphics; 0202 electrical engineering, electronic engineering, information engineering; Databases, Protein; Algorithms

We find recurring amino-acid residue packing patterns, or spatial motifs, that are characteristic of protein structural families, by applying a novel frequent subgraph mining algorithm to graph representations three-dimensional structure. Graph nodes represent amino acids, and edges chosen in one three ways: first, using threshold for contact distance between residues; second, Delaunay tessellation; third, the recently developed almost-Delaunay edges. For set graphs representing family from Structural Classification Proteins (SCOP) database, typically identi- fies several hundred common subgraphs corresponding motifs frequently found proteins but rarely outside it. some large map onto known functional regions two families explored this study, i.e., serine proteases kinases. based on significantly reduce number representation hence present computational advantage, yet patterns extracted such have biological interpretation approximately equivalent those graphs.