TY - CHAP

T1 - An overview and practical guide to building markov state models

AU - Bowman, Gregory R.

PY - 2014

Y1 - 2014

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84959197885&partnerID=8YFLogxK

U2 - 10.1007/978-94-7-7606-7_2

DO - 10.1007/978-94-7-7606-7_2

M3 - Chapter

C2 - 24297272

AN - SCOPUS:84959197885

SN - 9789400776050

T3 - Advances in Experimental Medicine and Biology

SP - 7

EP - 22

BT - An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation

PB - Springer New York LLC

ER -