A Bayesian Inference/Maximum Entropy Approach for Optimization and Validation of Empirical Molecular Models

Abstract

Accurate modeling of structural ensembles is essential for understanding molecular function, predicting molecular interactions, refining molecular potentials, protein engineering, drug discovery, and more. Here, we enhance molecular modeling through Bayesian Inference of Conformational Populations (BICePs), a highly versatile algorithm for reweighting simulated ensembles with experimental data. By incorporating replica-averaging, improved likelihood functions to better address systematic errors, and adopting variational optimization schemes, the utility of this algorithm in the refinement and validation of both structural ensembles and empirical models is unmatched. Utilizing a set of diverse experimental measurements, including NOE distances, chemical shifts, and vicinal J-coupling constants, we evaluated nine force fields for simulating the mini-protein chignolin, highlighting BICePs’ capability to correctly identify folded conformations and perform objective model selection. Additionally, we demonstrate how BICePs automates the parameterization of molecular potentials and forward models—computational frameworks that generate observable quantities—while properly accounting for all sources of random and systematic error. By reconciling prior knowledge of structural ensembles with solution-based experimental observations, BICePs not only offers a robust approach for evaluating the predictive accuracy of molecular models but also shows significant promise for future applications in computational chemistry and biophysics.