A kernel-based approach to molecular conformation analysis

Stefan Klus, Andreas Bittracher, Ingmar Schuster, Christof Schütte

Research output: Contribution to journalArticlepeer-review

13 Citations (Scopus)

Abstract

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.

Original languageEnglish
Article number244109
JournalJournal of Chemical Physics
Volume149
Issue number24
DOIs
Publication statusPublished - 28 Dec 2018

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

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