Binding proteins in the small world of residue networks /
Özer, Güngör (2004) Binding proteins in the small world of residue networks /. [Thesis]
Abstarct: We analyze the network properties of a set of 59 pairs of proteins in their bound and unbound forms. We verify that these "residue networks" are in the "small world" class in their separate forms as well as in complex. We also investigate the different network properties of interface residues compared to those of other surface residues of the complexes. The results point that the average shortest paths of interface residues are in general lower than other surface residues even in their unbound forms. Moreover, the residues that are used in the shortest pathways between the receptor and the ligand are analyzed with the theory of betweenness centrality. When specific weights are assigned to the links in the network, the same pairs of residue types emerge as important hubs when complexation occurs. The calculations are further implemented to decoy structures of 15 of the bound complexes, are further implemented to decoy structures of 15 of the bound complexes, with 10 decoys for each complex. We find the characteristic path length as the most important descriptor for differentiating between decoys and native structures.
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