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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.
Gogolinska, Anna 1, 2 ; Jakubowski, Rafal 1 ; Nowak, Wieslaw 1
@article{RO_2016__50_2_401_0,
author = {Gogolinska, Anna and Jakubowski, Rafal and Nowak, Wieslaw},
title = {Petri nets formalism facilitates analysis of complex biomolecular structural data},
journal = {RAIRO - Operations Research - Recherche Op\'erationnelle},
pages = {401--411},
publisher = {EDP-Sciences},
volume = {50},
number = {2},
year = {2016},
doi = {10.1051/ro/2015043},
zbl = {1338.90078},
mrnumber = {3479879},
language = {en},
url = {http://geodesic.mathdoc.fr/articles/10.1051/ro/2015043/}
}
TY - JOUR AU - Gogolinska, Anna AU - Jakubowski, Rafal AU - Nowak, Wieslaw TI - Petri nets formalism facilitates analysis of complex biomolecular structural data JO - RAIRO - Operations Research - Recherche Opérationnelle PY - 2016 SP - 401 EP - 411 VL - 50 IS - 2 PB - EDP-Sciences UR - http://geodesic.mathdoc.fr/articles/10.1051/ro/2015043/ DO - 10.1051/ro/2015043 LA - en ID - RO_2016__50_2_401_0 ER -
%0 Journal Article %A Gogolinska, Anna %A Jakubowski, Rafal %A Nowak, Wieslaw %T Petri nets formalism facilitates analysis of complex biomolecular structural data %J RAIRO - Operations Research - Recherche Opérationnelle %D 2016 %P 401-411 %V 50 %N 2 %I EDP-Sciences %U http://geodesic.mathdoc.fr/articles/10.1051/ro/2015043/ %R 10.1051/ro/2015043 %G en %F RO_2016__50_2_401_0
Gogolinska, Anna; Jakubowski, Rafal; Nowak, Wieslaw. Petri nets formalism facilitates analysis of complex biomolecular structural data. RAIRO - Operations Research - Recherche Opérationnelle, Special issue: Research on Optimization and Graph Theory dedicated to COSI 2013 / Special issue: Recent Advances in Operations Research in Computational Biology, Bioinformatics and Medicine, Tome 50 (2016) no. 2, pp. 401-411. doi: 10.1051/ro/2015043
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