title: Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics.
abstract: To meet the challenge of modeling the conformational dynamics of biological macromolecules over long time scales, much recent effort has been devoted to constructing stochastic kinetic models, often in the form of discrete-state Markov models, from short molecular dynamics simulations. To construct useful models that faithfully represent dynamics at the time scales of interest, it is necessary to decompose configuration space into a set of kinetically metastable states. Previous attempts to define these states have relied upon either prior knowledge of the slow degrees of freedom or on the application of conformational clustering techniques which assume that conformationally distinct clusters are also kinetically distinct. Here, we present a first version of an automatic algorithm for the discovery of kinetically metastable states that is generally applicable to solvated macromolecules. Given molecular dynamics trajectories initiated from a well-defined starting distribution, the algorithm discovers long lived, kinetically metastable states through successive iterations of partitioning and aggregating conformation space into kinetically related regions. The authors apply this method to three peptides in explicit solvent-terminally blocked alanine, the 21-residue helical F(s) peptide, and the engineered 12-residue beta-hairpin trpzip2-to assess its ability to generate physically meaningful states and faithful kinetic models.
authors.affiliation: Graduate Group in Biophysics, University of California-San Francisco, San Francisco, CA 94143, USA.
authors.forename: John D
authors.initials: JD
authors.lastname: Chodera
authors.forename: Nina
authors.initials: N
authors.lastname: Singhal
authors.forename: Vijay S
authors.initials: VS
authors.lastname: Pande
authors.forename: Ken A
authors.initials: KA
authors.lastname: Dill
authors.forename: William C
authors.initials: WC
authors.lastname: Swope
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D001704:Biopolymers / Q000737:chemistry*; D003198:Computer Simulation; D046911:Macromolecular Substances / Q000737:chemistry*; D008390:Markov Chains; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D010363:Pattern Recognition, Automated / Q000379:methods*; D044367:Phase Transition
chemical_list: D001704:Biopolymers; D046911:Macromolecular Substances