Umbrella Refinement of Ensembles-An Alternative View of Ensemble Optimization.

ABSTRACT: The elucidation of protein dynamics, especially in the context of intrinsically disordered proteins, is challenging and requires cooperation between experimental studies and computational analysis. Molecular dynamics simulations are an essential investigation tool but often struggle to accurately quantify the conformational preferences of flexible proteins. To create a quantitatively validated conformational ensemble, such simulations may be refined with experimental data using Bayesian and maximum entropy methods. In this study, we present a method to optimize a conformational ensemble using Bayes' theorem in connection with a methodology derived from Umbrella Sampling. The resulting method, called the Umbrella Refinement of Ensembles (URE), reduces the number of parameters to be optimize

SUBMITTER: Stockelmaier J 

PROVIDER: S-EPMC12156320 | biostudies-literature | 2025 Jun

REPOSITORIES: biostudies-literature