Multi-particle Brownian Dynamics software ProKSim for protein-protein interactions modeling

Khruschev S.S., Abaturova A.M., Diakonova A.N., Ustinin D.M., Zlenko D.V., Fedorov V.A., Kovalenko I.B., Riznichenko G.Yu., Rubin A.B.
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Protein-protein interactions are of central importance for virtually every process in living matter. Modeling the dynamics of protein association is crucial for understanding their functionality. This paper proposes novel simulation software ProKSim (Protein Kinetics Simulator) for modeling of protein interactions by means of the multi-particle Brownian Dynamics. Effect of long-range electrostatic interactions on the process of transient encounter complex formation is numerically estimated. Investigation of transient encounter complex formation was performed for three pairs of proteins: ferredoxin and ferredoxin:NADP+-redustase, plastocyanin and cytochrome f, barnase and barstar.

Keywords: multi-particle Brownian Dynamics, protein-protein recognition, molecular recognition
Citation in English: Khruschev S.S., Abaturova A.M., Diakonova A.N., Ustinin D.M., Zlenko D.V., Fedorov V.A., Kovalenko I.B., Riznichenko G.Yu., Rubin A.B. Multi-particle Brownian Dynamics software ProKSim for protein-protein interactions modeling // Computer Research and Modeling, 2013, vol. 5, no. 1, pp. 47-64
Citation in English: Khruschev S.S., Abaturova A.M., Diakonova A.N., Ustinin D.M., Zlenko D.V., Fedorov V.A., Kovalenko I.B., Riznichenko G.Yu., Rubin A.B. Multi-particle Brownian Dynamics software ProKSim for protein-protein interactions modeling // Computer Research and Modeling, 2013, vol. 5, no. 1, pp. 47-64
DOI: 10.20537/2076-7633-2013-5-1-47-64
URL: http://crm-en.ics.org.ru/journal/article/1989/
Creative Commons License This work is licensed under a Creative Commons Attribution-NoDerivs 3.0 Unported License.
According to Crossref, this article is cited by:
  • A N Diakonova, S S Khrushchev, I B Kovalenko, G Yu Riznichenko, A B Rubin. Influence of pH and ionic strength on electrostatic properties of ferredoxin, FNR, and hydrogenase and the rate constants of their interaction. // Physical Biology. — 2016. — V. 13, no. 5. — P. 056004. DOI: 10.1088/1478-3975/13/5/056004
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