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J Chem Phys. 2018 Dec 28;149(24):244109. doi: 10.1063/1.5063533.

A kernel-based approach to molecular conformation analysis.

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Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany.
Zalando Research, 11501 Berlin, Germany.


We present a novel machine learning approach to understand conformation dynamics of biomolecules. The approach combines kernel-based techniques that are popular in the machine learning community with transfer operator theory for analyzing dynamical systems in order to identify conformation dynamics based on molecular dynamics simulation data. We show that many of the prominent methods like Markov state models, extended dynamic mode decomposition (EDMD), and time-lagged independent component analysis (TICA) can be regarded as special cases of this approach and that new efficient algorithms can be constructed based on this derivation. The results of these new powerful methods will be illustrated with several examples, in particular, the alanine dipeptide and the protein NTL9.

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