Titlebook: An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation; Gregory R. Bowman,Vijay S. Pande,Fran

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Estimation and Validation of Markov Models,and approaches to validate whether this estimate is consistent with the simulation data at hand..Part of this chapter is reprinted with permission from Prinz et al. (Markov models of molecular kinetics: Generation and validation. J. Chem. Phys. 134:174,105, .). Copyright 2011, American Institute of Physics.

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https://doi.org/10.1007/978-3-211-78654-3A brief introduction to Markov state models and the organization of this book.

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https://doi.org/10.1007/978-3-642-90966-5An overview of the theory for analyzing the statistical properties of the reactive trajectories by which transitions occur between a set of initial and final states in a Markov model, and thereby obtain e.g. the highest flux pathways between these states.

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https://doi.org/10.1007/978-3-663-04667-7Understanding how proteins assemble into their final shapes (or “fold”) has been a grand challenge of computational biology for decades. MSM methods have allowed, for the first time, the direct simulation of how proteins fold on the microsecond to 10’s of millisecond timescale, yielding novel insight into the process.

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Introduction and Overview of This Book,A brief introduction to Markov state models and the organization of this book.

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Gregory R. Bowman,Vijay S. Pande,Frank NoéIn-depth review of the mathematical underpinnings of Markov state models.Practical insight into applying Markov state models to molecular systems.Points readers to freely available software for constr