Regensburg 2019 – scientific programme
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BP: Fachverband Biologische Physik
BP 1: Protein structure and dynamics
BP 1.2: Talk
Monday, April 1, 2019, 10:00–10:15, H4
A Coarse-Grained Network Description of Protein Tertiary Structure — •Nora Martin1,2 and Sebastian Ahnert1,2 — 1Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, Cambridge, UK — 2Sainsbury Laboratory, University of Cambridge, Cambridge, UK
Due to the complexity of protein tertiary structure, many methods of describing, classifying and comparing solved structures have been proposed. Network-based descriptions, known as protein structure networks, amino acid networks or protein contact maps, have been used successfully. There is some regularity and redundancy in protein structure networks: two segments of the polypeptide chain, which are close in the native structure, give rise to a group of edges in the contact network. We identify these groups of edges to coarse-grain and simplify protein structure networks. First, the network is compressed: a shorter encoding of a protein structure network is found by sorting network edges into groups. Then, a minimal network is constructed by choosing all nodes of the full network, but only one edge per group. In this contribution, we will present the construction of these coarse-grained networks and how they can be used to compare protein structures.