Multi-particle Brownian Dynamics software ProKSim for protein-protein interactions modeling
oleh: Sergey Sergeevich Khruschev, A. M. Abaturova, Aleksandra Nikitichna Diakonova, Dmitry Mikhailovitch Ustinin, D. V. Zlenko, Vladimir Andreevich Fedorov, I. B. Kovalenko, Galina Yu. Riznichenko, Andrei B. Rubin
| Format: | Article |
|---|---|
| Diterbitkan: | Institute of Computer Science 2013-02-01 |
Deskripsi
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.