ArticleThe Journal of chemical physics2013
On the statistical equivalence of restrained-ensemble simulations with the maximum entropy method.
Article in The Journal of chemical physics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 101 papers.
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101 citing papers in PubMed.
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- Automatic forward model parameterization with Bayesian inference of conformational populations.APL machine learning · 2026Article
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- NEAT-DNA: A Chemically Accurate, Sequence-Dependent Coarse-Grained Model for Large-Scale DNA Simulations.bioRxiv : the preprint server for biology · 2025Article
- FINCHES: A Computational Framework for Predicting Intermolecular Interactions in Intrinsically Disordered Proteins.International journal of molecular sciences · 2025Review
- Automatic Forward Model Parameterization with Bayesian Inference of Conformational Populations.ArXiv · 2025Article
- Ensemble refinement of mismodeled cryo-EM RNA structures using all-atom simulations.Nature communications · 2025Article
- Toward Predictive Coarse-Grained Simulations of Biomolecular Condensates.Biochemistry · 2025Review
- Energy landscape analysis of the development of the chromosome structure across the cell cycle.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Integrative spatiotemporal modeling of biomolecular processes: Application to the assembly of the nuclear pore complex.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Implementation of Time-Averaged Restraints with UNRES Coarse-Grained Model of Polypeptide Chains.Journal of chemical theory and computation · 2025Article
- Frontiers in integrative structural modeling of macromolecular assemblies.QRB discovery · 2025Review
- Integrative Modeling of 3D Genome Organization by Bayesian Molecular Dynamics Simulations with Hi-C Metainference.Methods in molecular biology (Clifton, N.J.) · 2025Article
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41 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
An issue of general interest in computer simulations is to incorporate information from experiments into a structural model. An important caveat in pursuing this goal is to avoid corrupting the resulting model with spurious and arbitrary biases. While the problem of biasing thermodynamic ensembles can be formulated rigorously using the maximum entropy method introduced by Jaynes, the approach can be cumbersome in practical applications with the need to determine multiple unknown coefficients iteratively. A popular alternative strategy to incorporate the information from experiments is to rely on restrained-ensemble molecular dynamics simulations. However, the fundamental validity of this computational strategy remains in question. Here, it is demonstrated that the statistical distribution produced by restrained-ensemble simulations is formally consistent with the maximum entropy method of Jaynes. This clarifies the underlying conditions under which restrained-ensemble simulations will yield results that are consistent with the maximum entropy method.
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