Analysis of Molecular Structure Data]{Systematic Study of Different Design Decisions in Markov Model-based Analysis of Molecular Structure Data: Extended Abstract

Modeling and simulation software now provide us with a view of the structure space navigated by peptides and proteins under physiological conditions. Such software, such as Molecular Dynamics, yields trajectories of consecutive structures accessed by a dynamic molecule, but does not readily expose the underlying organization in the structure state so as to summarize the equilibrium dynamics over the present structural states. In this paper we investigate Markov State Models on their ability to do so. While we make use of an established software to do so, we analyze within it different design decisions and measure their impact on the obtained results. We present our findings on optimal design decisions, revealing in the process the dynamics of the Met-enkephaline peptide.