Partial least-squares functional mode analysis: application to the membrane proteins AQP1, Aqy1, and CLC-ec1.

ABSTRACT: We introduce an approach based on the recently introduced functional mode analysis to identify collective modes of internal dynamics that maximally correlate to an external order parameter of functional interest. Input structural data can be either experimentally determined structure ensembles or simulated ensembles, such as molecular dynamics trajectories. Partial least-squares regression is shown to yield a robust solution to the multidimensional optimization problem, with a minimal and controllable risk of overfitting, as shown by extensive cross-validation. Several examples illustrate that the partial least-squares-based functional mode analysis successfully reveals the collective dynamics underlying the fluctuations in selected functional order parameters. Applications to T4 lysozyme,

SUBMITTER: Krivobokova T 

PROVIDER: S-EPMC3443789 | biostudies-literature | 2012 Aug

REPOSITORIES: biostudies-literature