title: Graph theoretic properties of networks formed by the Delaunay tessellation of protein structures.
abstract: The Delaunay tessellation of several sets of real and simplified model protein structures has been used to explore graph theoretic properties of residue contact networks. The system of contacts defined by residues joined by edges in the Delaunay simplices can be thought of as a graph or network and analyzed using techniques from elementary graph theory and the theory of complex networks. Such analysis indicates that protein contact networks have small world character, but technically are not small world networks. This approach also indicates that networks formed by native structures and by most misfolded decoys can be differentiated by their respective graph properties. The characteristic features of residue contact networks can be used for the detection of structural elements in proteins, such as the ubiquitous closed loops consisting of 22-32 consecutive residues, where terminal residues are Delaunay neighbors.
authors.affiliation: Laboratory for Structural Bioinformatics, School of Computational Sciences, George Mason University, 10900 University Boulevard MSN5B3, Manassas, VA 20110, USA.
authors.forename: Todd J
authors.initials: TJ
authors.lastname: Taylor
authors.forename: Iosif I
authors.initials: II
authors.lastname: Vaisman
mesh_terms: D001665:Binding Sites; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D046912:Multiprotein Complexes / Q000737:chemistry* / Q000648:ultrastructure*; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure*
chemical_list: D046912:Multiprotein Complexes; D011506:Proteins