ArticleBiophysical journal2014
Bayesian energy landscape tilting: towards concordant models of molecular ensembles.
Article in Biophysical journal, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- AI-Physics-Experiment Trinity for Integrated Protein Dynamics Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Minimum-Excess-Work Guidance: Score-Based Sampling with Experimental Data or Sparse Restraints.Journal of chemical theory and computation · 2026Article
- Computational Methods to Investigate Intrinsically Disordered Proteins and their Complexes.ArXiv · 2024Article
- BICePs v2.0: Software for Ensemble Reweighting Using Bayesian Inference of Conformational Populations.Journal of chemical information and modeling · 2023Article
- Reweighting methods for elucidation of conformation ensembles of proteins.Current opinion in structural biology · 2022Review
- Refining conformational ensembles of flexible proteins against small-angle x-ray scattering data.Biophysical journal · 2021Article
- Consistent Force Field Captures Homologue-Resolved HP1 Phase Separation.Journal of chemical theory and computation · 2021Article
- Using Cross-Correlated Spin Relaxation to Characterize Backbone Dihedral Angle Distributions of Flexible Protein Segments.Chemphyschem : a European journal of chemical physics and physical chemistry · 2021Article
- Integrating NMR and simulations reveals motions in the UUCG tetraloop.Nucleic acids research · 2020Article
- Maximum Entropy Optimized Force Field for Intrinsically Disordered Proteins.Journal of chemical theory and computation · 2020Article
- Experimentally Derived and Computationally Optimized Backbone Conformational Statistics for Blocked Amino Acids.Journal of chemical theory and computation · 2019Article
- Toward Learned Chemical Perception of Force Field Typing Rules.Journal of chemical theory and computation · 2019Article
- Refinement of Peptide Conformational Ensembles by 2D IR Spectroscopy: Application to Ala‒Ala‒Ala.Biophysical journal · 2018Article
- Model Selection Using BICePs: A Bayesian Approach for Force Field Validation and Parameterization.The journal of physical chemistry. B · 2018Article
- LinkingeLife · 2018Article
- Combining experimental and simulation data of molecular processes via augmented Markov models.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Refining Disordered Peptide Ensembles with Computational Amide I Spectroscopy: Application to Elastin-Like Peptides.The journal of physical chemistry. B · 2016Article
- Consistent View of Polypeptide Chain Expansion in Chemical Denaturants from Multiple Experimental Methods.Journal of the American Chemical Society · 2016Article
- ENCORE: Software for Quantitative Ensemble Comparison.PLoS computational biology · 2015Article
- Unveiling Inherent Degeneracies in Determining Population-Weighted Ensembles of Interdomain Orientational Distributions Using NMR Residual Dipolar Couplings: Application to RNA Helix Junction Helix Motifs.The journal of physical chemistry. B · 2015Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Predicting biological structure has remained challenging for systems such as disordered proteins that take on myriad conformations. Hybrid simulation/experiment strategies have been undermined by difficulties in evaluating errors from computational model inaccuracies and data uncertainties. Building on recent proposals from maximum entropy theory and nonequilibrium thermodynamics, we address these issues through a Bayesian energy landscape tilting (BELT) scheme for computing Bayesian hyperensembles over conformational ensembles. BELT uses Markov chain Monte Carlo to directly sample maximum-entropy conformational ensembles consistent with a set of input experimental observables. To test this framework, we apply BELT to model trialanine, starting from disagreeing simulations with the force fields ff96, ff99, ff99sbnmr-ildn, CHARMM27, and OPLS-AA. BELT incorporation of limited chemical shift and (3)J measurements gives convergent values of the peptide's α, β, and PPII conformational populations in all cases. As a test of predictive power, all five BELT hyperensembles recover set-aside measurements not used in the fitting and report accurate errors, even when starting from highly inaccurate simulations. BELT's principled framework thus enables practical predictions for complex biomolecular systems from discordant simulations and sparse data.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.