Method of prediction and optimization of conformational motion of proteins based on mass transportation principle

Abstract

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.