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Projected and Hidden Markov Models for calculating kinetics and metastable states of complex molecules
Frank Noe, Hao Wu, Jan-Hendrik Prinz +1
Markov state models (MSMs) have been successful in computing metastable states, slow relaxation timescales and associated structural changes, and stationary or kinetic experimental…
Spatiotemporal model of a key step in endocytosis: SNX9 recruitment via phosphoinositides
Johannes Schöneberg, Alexander Ullrich, York Posor +2
Clathrin mediated endocytosis (CME) is an ubiquitous cellular pathway that regulates central aspects of cell physiology such as nutrient uptake, modulation of signal transduction,…
Identification of slow molecular order parameters for Markov model construction
Guillermo Perez-Hernandez, Fabian Paul, Toni Giorgino +2
A goal in the kinetic characterization of a macromolecular system is the description of its slow relaxation processes, involving (i) identification of the structural changes involv…
Efficient Bayesian estimation of Markov model transition matrices with given stationary distribution
Benjamin Trendelkamp-Schroer, Frank Noe
Direct simulation of biomolecular dynamics in thermal equilibrium is challenging due to the metastable nature of conformation dynamics and the computational cost of molecular dynam…