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J Chem Theory Comput. 2018 Dec 11;14(12):6623-6631. doi: 10.1021/acs.jctc.8b00733. Epub 2018 Nov 30.

Protein Residue Networks from Energetic and Geometric Data: Are They Identical?

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Institute of Chemistry - Centre for Glycomics , Dubravska cesta 9 , 84538 Bratislava , Slovakia.
Agency for Medical Research and Development (AMED) , Chiyoda-ku , Japan.
Department of Chemistry , Rikkyo University , Nishi-Ikebukuro , Toshima, Tokyo 171-8501 , Japan.
Department of Internal Medicine, Faculty of Medicine , University of Tsukuba , 1-1-1 Tennodai , Tsukuba, Ibaraki 305-8575 , Japan.
Center for Computational Sciences , University of Tsukuba , Tennodai 1-1-1 , Tsukuba, Ibaraki 305-8577 , Japan.


Protein residue networks (PRN) from energetic and geometric data are probably not identical. PRNs constructed from ab initio pair interaction energies are analyzed for the first time and compared to PRN based on center of mass separation. We use modern, previously unused algorithms such as global and local efficiencies to quantitatively confirm that both types of PRNs do exhibit small-world character. The main novelty finding is that interaction energy-based PRNs preserve small-world character even when clustered. A node hierarchy independent of the cutoff energy used for the edge creation is characteristic for them. Efficiency centrality identifies hubs responsible for such behavior. The interaction energy-based PRNs seem to comply with the scale-free network model with respect to efficiency centrality distribution as opposed to distance based PRNs. Community detection is introduced into protein network research as an extension beyond cluster analysis to study tertiary and quaternary structures.

[Indexed for MEDLINE]

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