EMMA: A Software Package for Markov Model Building and Analysis

Citations Over TimeTop 10% of 2012 papers

Abstract

The study of folding and conformational changes of macromolecules by molecular dynamics simulations often requires the generation of large amounts of simulation data that are difficult to analyze. Markov (state) models (MSMs) address this challenge by providing a systematic way to decompose the state space of the molecular system into substates and to estimate a transition matrix containing the transition probabilities between these substates. This transition matrix can be analyzed to reveal the metastable, i.e., long-living, states of the system, its slowest relaxation time scales, and transition pathways and rates, e.g., from unfolded to folded, or from dissociated to bound states. Markov models can also be used to calculate spectroscopic data and thus serve as a way to reconcile experimental and simulation data. To reduce the technical burden of constructing, validating, and analyzing such MSMs, we provide the software framework EMMA that is freely available at https://simtk.org/home/emma .

Related Papers

• → Comparative Analysis of Markovian Methodologies for Modeling Infrastructure System Performance(2021)39 cited
• → Markov and semi-Markov models in system reliability(2023)11 cited
• → Multistate Markov Models and Structural Properties of the Transition-Rate Matrix(1986)38 cited
• → A Method to Simplify the Markov Model of Protective Systems(2022)