RT Journal Article SR Electronic T1 MSMBuilder: Statistical Models for Biomolecular Dynamics JF bioRxiv FD Cold Spring Harbor Laboratory SP 084020 DO 10.1101/084020 A1 Matthew P. Harrigan A1 Mohammad M. Sultan A1 Carlos X. Hernández A1 Brooke E. Husic A1 Peter Eastman A1 Christian R. Schwantes A1 Kyle A. Beauchamp A1 Robert T. McGibbon A1 Vijay S. Pande YR 2016 UL http://biorxiv.org/content/early/2016/10/27/084020.abstract AB MSMBuilder is a software package for building statistical models of high-dimensional time-series data. It is designed with a particular focus on the analysis of atomistic simulations of biomolecular dynamics such as protein folding and conformational change. MSMBuilder is named for its ability to construct Markov State Models (MSMs), a class of models that has gained favor among computational biophysicists. In addition to both well-established and newer MSM methods, the package includes complementary algorithms for understanding time-series data such as hidden Markov models (HMMs) and time-structure based independent component analysis (tICA). MSMBuilder boasts an easy to use command-line interface, as well as clear and consistent abstractions through its Python API (application programming interface). MSMBuilder is developed with careful consideration for compatibility with the broader machine-learning community by following the design of scikit-learn. The package is used primarily by practitioners of molecular dynamics but is just as applicable to other computational or experimental time-series measurements. http://msmbuilder.org