MSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond Scale
2011; American Chemical Society; Volume: 7; Issue: 10 Linguagem: Inglês
10.1021/ct200463m
ISSN1549-9626
AutoresKyle A. Beauchamp, Gregory R. Bowman, Thomas J. Lane, Lutz Maibaum, Imran S. Haque, Vijay S. Pande,
Tópico(s)Microbial Metabolic Engineering and Bioproduction
ResumoMarkov State Models provide a framework for understanding the fundamental states and rates in the conformational dynamics of biomolecules. We describe an improved protocol for constructing Markov State Models from molecular dynamics simulations. The new protocol includes advances in clustering, data preparation, and model estimation; these improvements lead to significant increases in model accuracy, as assessed by the ability to recapitulate equilibrium and kinetic properties of reference systems. A high-performance implementation of this protocol, provided in MSMBuilder2, is validated on dynamics ranging from picoseconds to milliseconds.
Referência(s)