{"title":"Detecting Community Structure in Amino Acid Interaction Networks","authors":"Omar GACI, Stefan BALEV, Antoine DUTOT","volume":34,"journal":"International Journal of Computer and Information Engineering","pagesStart":2387,"pagesEnd":2395,"ISSN":"1307-6892","URL":"https:\/\/publications.waset.org\/pdf\/2391","abstract":"<p>In this paper we introduce the notion of protein interaction network. This is a graph whose vertices are the protein-s amino acids and whose edges are the interactions between them. Using a graph theory approach, we observe that according to their structural roles, the nodes interact differently. By leading a community structure detection, we confirm this specific behavior and describe thecommunities composition to finally propose a new approach to fold a protein interaction network.<\/p>\r\n","references":"[1] R. Albert, H. Jeong, and A.-L. Barab'asi. The diameter of the world wide web. Nature, 401:130-131, 1999.\r\n[2] A. R. Atilgan, P. Akan, and C. Baysal. Small-world communication of residues and significance for protein dynamics. Biophys J, 86(1 Pt\r\n1):85-91, January 2004.\r\n[3] R. Beatson and L. Greengard. A short course on fast multipole methods.\r\n[4] H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat,\r\nH. Weissig, I. N. Shindyalov, and P. E. Bourne. The protein data bank. Nucleic Acids Research, 28:235-242, 2000.\r\n[5] C. Branden and J. Tooze. Introduction to protein structure. Garland\r\nPublishing, 1999.\r\n[6] K. V. Brinda and S. Vishveshwara. A network representation of protein\r\nstructures: implications for protein stability. Biophys J, 89(6):4159-\r\n4170, December 2005.\r\n[7] A. Broder, R. Kumar, F. Maghoul, P. Raghavan, S. Rajagopalan, R. Stata,\r\nA. Tomkins, and J. Wiener. Graph structure in the Web. Computer Networks, 33(1-6):309-320, 2000.\r\n[8] Aaron Clauset, M. E. J. Newman, and Cristopher Moore. Finding\r\ncommunity structure in very large networks. Physical Review E,\r\n70:066111, 2004.\r\n[9] N. V. Dokholyan, L. Li, F. Ding, and E. I. Shakhnovich. Topological\r\ndeterminants of protein folding. Proc Natl Acad Sci U S A, 99(13):8637-\r\n8641, June 2002.\r\n[10] Thomas M. J. Fruchterman and Edward M. Reingold. Graph drawing\r\nby force-directed placement. Software - Practice and Experience,\r\n21(11):1129-1164, 1991.\r\n[11] O. Gaci and S. Balev. Hubs identification in amino acids interaction\r\nnetworks. In Proceedings of the 7th ACS\/IEEE International Conference\r\non Computer Systems and Applications, 2009. 7 pages.\r\n[12] O. Gaci and S. Balev. The small-world model for amino acid interaction\r\nnetworks. In Proceedings of the IEEE AINA 2009, workshop on\r\nBioinformatics and Life Science Modeling and Computing, 2009. 6\r\npages.\r\n[13] A. Ghosh, K. V. Brinda, and S. Vishveshwara. Dynamics of lysozyme\r\nstructure network: probing the process of unfolding. Biophys J,\r\n92(7):2523-2535, April 2007.\r\n[14] L. Greengard and V. Rokhlin. A fast algorithm for particle simulations.\r\nJ. Comput. Phys., 73(2):325-348, 1987.\r\n[15] H. Jeong, B. Tombor, R. Albert, Z. N. Oltvai, and A.-L. Barab'asi. The\r\nlarge-scale organization of metabolic networks. Nature, 407(6804):651-\r\n654, October 2000.\r\n[16] U. K. Muppirala and Z. Li. A simple approach for protein structure\r\ndiscrimination based on the network pattern of conserved hydrophobic\r\nresidues. Protein Eng Des Sel, 19(6):265-275, June 2006.\r\n[17] M. E. J. Newman. Fast algorithm for detecting community structure in\r\nnetworks. Physical Review E, 69:066133, 2004.\r\n[18] John P. Scott. Social Network Analysis: A Handbook. SAGE Publications,\r\nJanuary 2000.\r\n[19] S. Wasserman and K. Faust. Social network analysis : methods and\r\napplications , volume 8 of Structural analysis in the social sciences.\r\nCambridge University Press, Cambridge, 1994.\r\n[20] D. J. Watts and S. H. Strogatz. Collective dynamics of -small-world-\r\nnetworks. Nature., 393:440-442, 1998.\r\n[21] Bo Yang and Da You Liu. Incremental algorithm for detecting community structure in dynamic networks. In proceedings of the 4th International Conference on Machine Learning and Cybernetics, pages 2284-2290, August 2005. ","publisher":"World Academy of Science, Engineering and Technology","index":"Open Science Index 34, 2009"}