TitleOptimizing representations for integrative structural modeling using Bayesian model selection.
Publication TypeJournal Article
Year of Publication2024
AuthorsArvindekar S, Pathak AS, Majila K, Viswanath S
Date Published2024 Mar 04
KeywordsBayes Theorem, Benchmarking, Macromolecular Substances

MOTIVATION: Integrative structural modeling combines data from experiments, physical principles, statistics of previous structures, and prior models to obtain structures of macromolecular assemblies that are challenging to characterize experimentally. The choice of model representation is a key decision in integrative modeling, as it dictates the accuracy of scoring, efficiency of sampling, and resolution of analysis. But currently, the choice is usually made ad hoc, manually.

RESULTS: Here, we report NestOR (Nested Sampling for Optimizing Representation), a fully automated, statistically rigorous method based on Bayesian model selection to identify the optimal coarse-grained representation for a given integrative modeling setup. Given an integrative modeling setup, it determines the optimal representations from given candidate representations based on their model evidence and sampling efficiency. The performance of NestOR was evaluated on a benchmark of four macromolecular assemblies.

AVAILABILITY AND IMPLEMENTATION: NestOR is implemented in the Integrative Modeling Platform (https://integrativemodeling.org) and is available at https://github.com/isblab/nestor. Data for the benchmark is at https://www.doi.org/10.5281/zenodo.10360718.

Alternate JournalBioinformatics
PubMed ID38391029
PubMed Central IDPMC10924281
Grant ListR01 GM129325 / GM / NIGMS NIH HHS / United States
P41 RR001081 / RR / NCRR NIH HHS / United States