Geodesic
Construction of extended dynamical contact maps by molecular-dynamics simulation data
Matematičeskaâ biologiâ i bioinformatika, Tome 4 (2009) no. 1, pp. 36-45.

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The article describes algorithms for the construction of extended dynamical contact maps and the tape of contacts for the analyzing of dynamical molecular systems. This analyzis is based on TAMD program – Trajectory Analyzer of Molecular Dynamics. 
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I. V. Likhachev; N. K. Balabaev. Construction of extended dynamical contact maps by molecular-dynamics simulation data. Matematičeskaâ biologiâ i bioinformatika, Tome 4 (2009) no. 1, pp. 36-45. http://geodesic.mathdoc.fr/item/MBB_2009_4_1_a2/

[1] I. V. Likhachev, N. K. Balabaev, “Analizator traektorii molekulyarnoi dinamiki”, Matematicheskaya biologiya i bioinformatika, 2:1 (2007), 120–129 http://www.matbio.org/downloads/Likhachev2007(2_120).pdf

[2] Glyakina A. V., Galzitskaya O. V., Balabaev N. K., “Molekulyarnaya dinamika razvorachivaniya belkovykh globul pod deistviem vneshnikh sil”, Vestnik Tverskogo gosudarstvennogo universiteta, 68:8 (2008), 109–119