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J Phys Chem Lett. 2018 May 3;9(9):2144-2150. doi: 10.1021/acs.jpclett.8b00759. Epub 2018 Apr 12.

Machine Learning of Biomolecular Reaction Coordinates.

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Biomolecular Dynamics, Institute of Physics , Albert Ludwigs University , 79104 Freiburg , Germany.


We present a systematic approach to reduce the dimensionality of a complex molecular system. Starting with a data set of molecular coordinates (obtained from experiment or simulation) and an associated set of metastable conformational states (obtained from clustering the data), a supervised machine learning model is trained to assign unknown molecular structures to the set of metastable states. In this way, the model learns to determine the features of the molecular coordinates that are most important to discriminate the states. Using a new algorithm that exploits this feature importance via an iterative exclusion principle, we identify the essential internal coordinates (such as specific interatomic distances or dihedral angles) of the system, which are shown to represent versatile reaction coordinates that account for the dynamics of the slow degrees of freedom and explain the mechanism of the underlying processes. Moreover, these coordinates give rise to a free energy landscape that may reveal previously hidden intermediate states of the system.

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