Journal Article Spotting the difference in molecular dynamics simulations of biomolecules

櫻庭, 俊  ,  河野, 秀俊

145 ( 8 )  , p.074116 , 2016-08 , the AIP Publishing
Description
Comparing two trajectories from molecular simulations conducted under different conditions is not a trivial task. In this study, we apply a method called LDA-ITER to compare two molecular simulation results by finding the appropriate projection vectors. Because LDA-ITER attempts to determine a projection such that the projections of the two trajectories do not overlap, the comparison does not suffer from a strong anisotropy, which is an issue in protein dynamics. LDA-ITER is applied to two test cases: the T4 lysozyme protein simulation with or without a point mutation and the allosteric protein PDZ2 domain of hPTP1E with or without a ligand. The projection determined by the method agrees with the experimental data and previous simulations. The proposed procedure, which complements existing methods, is a versatile analytical method that is specialized to find the difference between two trajectories.

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