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Optimal Dimensionality Reduction of Multistate Kinetic and Markov-State Models

https://doi.org/10.1021/jp508375q
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Coarse Master Equation from Bayesian Analysis of Replica Molecular Dynamics Simulations
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Long-Time Conformational Transitions of Alanine Dipeptide in Aqueous Solution: Continuous and Discrete-State Kinetic Models
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Coarse Master Equations for Peptide Folding Dynamics
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SWARM-MD: Searching Conformational Space by Cooperative Molecular Dynamics
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Absolute comparison of simulated and experimental protein-folding dynamics
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Coarse molecular dynamics of a peptide fragment: Free energy, kinetics, and long-time dynamics computations
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A coarse graining method for the identification of transition rates between molecular conformations
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On the assumptions underlying milestoning
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A Bayesian method for construction of Markov models to describe dynamics on various time-scales
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The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics
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Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations
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Nonequilibrium Statistical Mechanics
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Parallel replica method for dynamics of infrequent events
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T RANSITION P ATH S AMPLING : Throwing Ropes Over Rough Mountain Passes, in the Dark

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