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Spectral reconstruction of protein contact networks.pdf

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Spectral reconstruction of protein contact networks.pdf

Physica A 471 (2017) 804–817 Contents lists available at ScienceDirect Physica A journal homepage: /locate/physa Spectral reconstruction of protein contact networks Enrico Maiorino a,*, Antonello Rizzi a, Alireza Sadeghian b, Alessandro Giulianic a Department of Information Engineering, Electronics, and Telecommunications, SAPIENZA University of Rome, Via Eudossiana 18, 00184 Rome, Italy b Department of Computer Science, Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada c Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy highlights ? Protein contact networks (PCN) have a characteristic Laplacian spectral density. ? We defined a procedure to generate networks with the same spectral density. ? The new networks (LMGRS-GEN) are topologically similar to PCN. ? Short-range eigenvalues correlations of LMGRS-GEN are compatible with PCN. article info Article history: Received 21 April 2016 Received in revised form 25 October 2016 Available online 22 December 2016 Keywords: Protein contact network Graph laplacian Graph spectra Random matrix theory Genetic algorithm abstract In this work, we present a method for generating an adjacency matrix encoding a typical protein contact network. This work constitutes a follow-up to our recent work (Livi et al., 2015), whose aim was to estimate the relative contribution of different topological features in discovering of the unique properties of protein structures. We perform a genetic algorithm based optimization in order to modify the matrices generated with the procedures explained in (Livi et al., 2015). Our objective here is to minimize the distance with respect to a target spectral density, which is elaborated using the normalized graph Laplacian representation of graphs. Such a target density is obtained by averaging the kernel-estimated densities of a class of experimental protein maps having different dimensions. This is possible given the bounded-dom