Modifying the DPClus algorithm for identifying protein complexes based on new topological structures

Background: Identification of protein complexes is crucial for understanding principles of cellular organization and functions. As the size of protein-protein interaction set increases, a general trend is to represent the interactions as a network and to develop effective algorithms to detect significant complexes in such networks. Results: Based on the study of known complexes in protein networks, this paper proposes a new topological structure for protein complexes, which is a combination of subgraph diameter (or average vertex distance) and subgraph density. Following the approach of that of the previously proposed clustering algorithm DPClus which expands clusters starting from seeded vertices, we present a clustering algorithm IPCA based on the new topological structure for identifying complexes in large protein interaction networks. The algorithm IPCA is applied to the protein interaction network of Sacchromyces cerevisiae and identifies many well known complexes. Experimental r...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Min Li, Jianer Chen, Jianxin Wang, Bin Hu, Gang Chen
• Keywords: Algorithm, BMCBI 2008, Protein, Protein Complexes