An overview and practical guide to building markov state models

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Abstract

Markov state models (MSMs) have a long history in the physical sciences, where they are often referred to as discrete-time master equation models. Therefore, there are many well-established ways of working with and analyzing these models given a valid set of states. However, defining a set of states sufficient for modeling complex molecular processes, like protein folding, is quite difficult. The main purpose of this chapter is to provide a practical guide to building MSMs, with an emphasis on partitioning a molecule's conformational space into a valid set of states. We will start off with a brief discussion of some of the major requirements for a valid state decomposition. Then we will move on to a more detailed discussion of each of the steps commonly used for building MSMs, including an overview of the various options at each stage and their relative merits. Finally, I will introduce a few advanced topics and conclude with some future directions.

Original languageEnglish
Title of host publicationAn Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation
PublisherSpringer New York LLC
Pages7-22
Number of pages16
ISBN (Print)9789400776050
DOIs
StatePublished - 2014

Publication series

NameAdvances in Experimental Medicine and Biology
Volume797
ISSN (Print)0065-2598

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