Progress and challenges in the automated construction of Markov state models for full protein systems.

ABSTRACT: Markov state models (MSMs) are a powerful tool for modeling both the thermodynamics and kinetics of molecular systems. In addition, they provide a rigorous means to combine information from multiple sources into a single model and to direct future simulations/experiments to minimize uncertainties in the model. However, constructing MSMs is challenging because doing so requires decomposing the extremely high dimensional and rugged free energy landscape of a molecular system into long-lived states, also called metastable states. Thus, their application has generally required significant chemical intuition and hand-tuning. To address this limitation we have developed a toolkit for automating the construction of MSMs called MSMBUILDER (available at https://simtk.org/home/msmbuilder). In this w

SUBMITTER: Bowman GR 

PROVIDER: S-EPMC2766407 | biostudies-literature | 2009 Sep

REPOSITORIES: biostudies-literature