title: Spotting the difference in molecular dynamics simulations of biomolecules.
abstract: Comparing two trajectories from molecular simulations conducted under different conditions is not a trivial task. In this study, we apply a method called Linear Discriminant Analysis with ITERative procedure (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.
authors.affiliation: Molecular Modeling and Simulation Group, Quantum Beam Science Center, Japan Atomic Energy Agency, 8-1-7 Umemidai, Kidugawa, Kyoto 619-0215, Japan.
authors.forename: Shun
authors.initials: S
authors.lastname: Sakuraba
authors.affiliation: Molecular Modeling and Simulation Group, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kidugawa, Kyoto 619-0215, Japan.
authors.forename: Hidetoshi
authors.initials: H
authors.lastname: Kono
mesh_terms: D019295:Computational Biology; D056004:Molecular Dynamics Simulation