Abstract
In molecular dynamics, there can be conformational dynamics of molecules. To identify the conformational space, chemists take a serie of snapshots of molecule at regular time then they try to analyze them by their eyes. When a serie contains thousands of snapshots or when the molecule is very big, this work is not possible. We present a new algorithm which aims to analyze the evolution of molecules under specific environmental conditions and characterize and quantify the isomers (conformations that could take a molecule). The algorithm is based on graph theory, it uses the distance geometry and some chemical properties (covalent bonds, H-bonds, proton transfer...). Optimizations were done to the algorithm to let it faster an efficient and to have a good time complexity. It can handle series with thousands of snapshots of molecules in Gas phase and analyze them in a few milliseconds.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Cimas, A., Vaden, T., De Boer, T., Snoek, L., Gaigeot, M.-P.: Vibrational spectra of small protonated peptides from finite temperature md simulations and irmpd spectroscopy. J. Chem. Theory Comput. 5(4), 1068–1078 (2009)
Dennington, R., Keith, T., Millam, J., Eppinnett, K., Hovell, W.L., Gilliland, R.: Gaussview. Semichem Inc., Shawnee Mission (2009)
Hanwell, M.D., Curtis, D.E., Lonie, D.C., Vandermeersch, T., Zurek, E., Hutchison, G.R.: Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. J. Cheminform. 4, 17 (2012)
Humphrey, W., Dalke, A., Schulten, K.: Vmd: visual molecular dynamics. J. Mol. Graph. 14(1), 33–38 (1996)
Mooney, B.L., Corrales, L.R., Clark, A.E.: MoleculaRnetworks: an integrated graph theoretic and data mining tool to explore solvent organization in molecular simulation. J. Comput. Chem. 33(8), 853–860 (2012)
Ozkanlar, A., Clark, A.E.: ChemNetworks: a complex network analysis tool for chemical systems. J. Comput. Chem. 35(6), 495–505 (2014)
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2016 Springer International Publishing Switzerland
About this paper
Cite this paper
Barth, D., Bougueroua, S., Gaigeot, MP., Quessette, F., Spezia, R., Vial, S. (2016). A New Graph Algorithm for the Analysis of Conformational Dynamics of Molecules. In: Abdelrahman, O., Gelenbe, E., Gorbil, G., Lent, R. (eds) Information Sciences and Systems 2015. Lecture Notes in Electrical Engineering, vol 363. Springer, Cham. https://doi.org/10.1007/978-3-319-22635-4_29
Download citation
DOI: https://doi.org/10.1007/978-3-319-22635-4_29
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-22634-7
Online ISBN: 978-3-319-22635-4
eBook Packages: EngineeringEngineering (R0)