Petri nets formalism facilitates analysis of complex biomolecular structural data
RAIRO - Operations Research - Recherche Opérationnelle, Volume 50 (2016) no. 2, pp. 401-411.

Molecular dynamics (MD) simulation is a popular method of protein and nucleic acids research. Current MD output trajectories are huge files and therefore they are hard to analyze. Petri nets (PNs) is a mathematical modeling language that allows for concise, graphical representation of complex data. We have developed a few algorithms for PNs generation from such large MD trajectories. One of them, called the One Place One Conformation (OPOC) algorithm, is presented in a greater detail. In the OPOC algorithm one biomolecular conformation corresponds to one PN place and a transition occurring in PN graph is related to a change between biomolecules conformations. As case studies three simulations are analyzed: an enforced steered MD (SMD) dissociation of a transthyretin protein tetramer into dimers, the SMD dissociation of an antibody-antigen complex and a classical MD simulation of transthyretin. We show that PNs reproduce events hidden in MD trajectories and enable observations of the conformational space features hard-to-see by the other clustering methods. Thus, a fundamental process of biomolecular data classification may be optimized using the PN approach.

DOI: 10.1051/ro/2015043
Classification: 90B10, 68W99, 92-08
Keywords: Data mining, Petri net, molecular dynamic simulations, clustering, conformational space, graphs
Gogolinska, Anna 1, 2; Jakubowski, Rafal 1; Nowak, Wieslaw 1

1 Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Torun, Poland
2 Faculty of Mathematics and Computer Science, Nicolaus Copernicus University ul. Chopina 12/18, 87-100 Torun, Poland.
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Gogolinska, Anna; Jakubowski, Rafal; Nowak, Wieslaw. Petri nets formalism facilitates analysis of complex biomolecular structural data. RAIRO - Operations Research - Recherche Opérationnelle, Volume 50 (2016) no. 2, pp. 401-411. doi : 10.1051/ro/2015043. http://archive.numdam.org/articles/10.1051/ro/2015043/

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