Method of prediction and optimization of conformational motion of proteins based on mass transportation principle
The paper highlights approaches to fast prediction of protein conformational mobility. A new mathematical model based on the transportation principle is proposed. We describe an algorithm and soft-ware developed for a construction of the possible trajectories of the large-scale conformational motions of proteins (i.e. movements that occur within relatively large time intervals of the order of milliseconds). The modeling showed that the proposed method provides adequate, in terms of current knowledge of the biology and physics of proteins, results and allows simulation of large-scale conformational transitions for less time.
Keywordsconformational motion of protein transportation principle optimization coarse-grained methods
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- 2.G. Song and N. M. Amato, in Proc. ACM Int. Conf. on Computational Biology (RECOMB) (2001), pp. 287–296.Google Scholar
- 4.M. S. Apaydin, A. P. Singh, D. L. Brutlag, et al., in IEEE International Conference on Robotics and Automation, Ed. by A. Singh (IEEE Press, New York, 2001), pp. 932–939.Google Scholar
- 6.S. M. LaValle and J. J. Kuffner, in Algorithmic and Computational Robotics: New Directions, Ed. by B. Donald, K. Lynch, D. Rus (A.K. Peters, Wellesley, Massachusetts, 2001), pp. 293–308.Google Scholar
- 16.D. A. Case, in Rigidity Theory and Applications, Ed. by M. Thorpe, P. Duxbury (Springer, Fundamental Materials Research, 2002), pp. 329–344.Google Scholar
- 27.K. V. Shaitan, N. K. Balabaev, A. S. Lemak, et al., Biofizika 42, 47 (1997).Google Scholar
- 34.M. S. Apaydin, A. P. Singh, D. L. Brutlag, et al., in IEEE International Conference on Robotics and Automation, Ed. by A. Singh (IEEE Press, New York, 2001), pp. 932–939.Google Scholar
- 38.J. Cortes, L. Jaillet, and T. Simeon, in IEEE International Conference on Robotics and Automation (IEEE Press, New York, 2007), pp. 3301–3306.Google Scholar
- 39.L. C. Evans, in Partial Differential Equations and Monge-Kantorovich Mass Transfer. Current Developments in Mathematics (Cambridge, MA Int. Press, Boston, MA, 1999), pp. 65–126.Google Scholar
- 41.Yu. B. Porozov, A. A. Koshevoy, and E. O. Stepanov, Certificate of State Registration for Computer Software No. 2011619647. Registered 21.12.2011.Google Scholar