Spotting the difference in molecular dynamics simulations of biomolecules
In: J. Phys. Chem., Jg. 145 (2016-08-01), Heft 7, S. 074116-74116
Online
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Zugriff:
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.
Titel: |
Spotting the difference in molecular dynamics simulations of biomolecules
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Zeitschrift: | J. Phys. Chem., Jg. 145 (2016-08-01), Heft 7, S. 074116-74116 |
Veröffentlichung: | American Chemical Society, 2016 |
Medientyp: | unknown |
ISSN: | 0021-9606 (print) |
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