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• W4221008017 abstract "Abstract The increasing interest in modeling the dynamics of ever larger proteins has revealed a fundamental problem with models that describe the molecular system as being in a global configuration state. This notion limits our ability to gather sufficient statistics of state probabilities or state-to-state transitions because for large molecular systems the number of metastable states grows exponentially with size. In this manuscript, we approach this challenge by introducing a method that combines our recent progress on independent Markov decomposition (IMD) with VAMPnets, a deep learning approach to Markov modeling. We establish a training objective that quantifies how well a given decomposition of the molecular system into independent subdomains with Markovian dynamics approximates the overall dynamics. By constructing an end-to-end learning framework, the decomposition into such subdomains and their individual Markov state models are simultaneously learned, providing a data-efficient and easily interpretable summary of the complex system dynamics. While learning the dynamical coupling between Markovian subdomains is still an open issue, the present results are a significant step towards learning “Ising models” of large molecular complexes from simulation data." @default.
• W4221008017 created "2022-04-03" @default.
• W4221008017 creator A5014208179 @default.
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• W4221008017 date "2022-03-31" @default.
• W4221008017 modified "2023-09-24" @default.
• W4221008017 title "Deep learning to decompose macromolecules into independent Markovian domains" @default.
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• W4221008017 doi "https://doi.org/10.1101/2022.03.30.486366" @default.
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