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On Combinatorial Optimisation in Analysis of Protein-Protein Interaction and Protein Folding Networks

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Applications of Evolutionary Computation (EvoApplications 2016)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 9597))

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Abstract

Protein-protein interaction networks and protein folding networks represent prominent research topics at the intersection of bioinformatics and network science. In this paper, we present a study of these networks from combinatorial optimisation point of view. Using a combination of classical heuristics and stochastic optimisation techniques, we were able to identify several interesting combinatorial properties of biological networks of the COSIN project. We obtained optimal or near-optimal solutions to maximum clique and chromatic number problems for these networks. We also explore patterns of both non-overlapping and overlapping cliques in these networks. Optimal or near-optimal solutions to partitioning of these networks into non-overlapping cliques and to maximum independent set problem were discovered. Maximal cliques are explored by enumerative techniques. Domination in these networks is briefly studied, too. Applications and extensions of our findings are discussed.

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Authors and Affiliations

  1. Department of Computer Science, University of Hull, Cottingham Road, Hull, HU6 7RX, UK

    David Chalupa

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  1. David Chalupa
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Correspondence to David Chalupa .

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Editors and Affiliations

  1. Politecnico di Torino, Turin, Italy

    Giovanni Squillero

  2. Aalborg University, Copenhagen, Denmark

    Paolo Burelli

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Chalupa, D. (2016). On Combinatorial Optimisation in Analysis of Protein-Protein Interaction and Protein Folding Networks. In: Squillero, G., Burelli, P. (eds) Applications of Evolutionary Computation. EvoApplications 2016. Lecture Notes in Computer Science(), vol 9597. Springer, Cham. https://doi.org/10.1007/978-3-319-31204-0_7

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  • DOI: https://doi.org/10.1007/978-3-319-31204-0_7

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