A tutorial on building markov state models with MSMBuilder and coarse-graining them with BACE.
Markov state models (MSMs) are a powerful means of (1) making sense of molecular simulations, (2) making a quantitative connection between simulation and experiment, and (3) driving efficient simulations. A Markov model can be thought of as a map of the conformational space a molecule explores. Instead of having towns and cities connected with roads labeled with speed limits, a Markov model has conformational states and probabilities of transitioning between pairs of these states. This tutorial describes how to build Markov models and a few of the basic analyses that can be performed with the MSMBuilder software package.
Departments of Molecular & Cell Biology and Chemistry, University of California, Berkeley, Berkeley, CA, USA.
Gregory R
GR
Bowman
D019295:Computational Biology / Q000379:methods; D020407:Internet; D008390:Markov Chains; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry*; D012984:Software
D011506:Proteins