ArticleNature communications2025
Determining accurate conformational ensembles of intrinsically disordered proteins at atomic resolution.
Article in Nature communications, 2025. 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.
- Antibody-drug conjugate engineering: from design to efficacy and safety.Signal transduction and targeted therapy · 2026Review
- Beyond the structure-function paradigm: A comprehensive review of intrinsically disordered proteins.Biochemistry and biophysics reports · 2026Review
- A Bayesian Approach to Interpret Time-Resolved Experiments Using Molecular Simulations.ACS physical chemistry Au · 2026Article
- Complete NMR assignment for 275 of the most common dipeptides in intrinsically disordered proteins.Scientific data · 2026Article
- From possibility to precision in macromolecular ensemble prediction.Nature methods · 2026Review
- Sketching microprotein portraits.Protein science : a publication of the Protein Society · 2026Review
- Transient tertiary structure in intrinsically disordered proteins revealed by multithermal enhanced sampling.Nature communications · 2026Article
- Backbone rigidity of disordered protein linkers from NMR experiments and MD simulations.Biophysical journal · 2026Article
- Toward a unified framework for determining conformational ensembles of disordered proteins.Nature methods · 2026Review
- Article
- Evaluating the Impact of Phosphorylation on the Dynamics of the Tau Protein Proline-Rich Region.Journal of chemical theory and computation · 2026Article
- Atomic resolution ensembles of intrinsically disordered proteins with Alphafold.Nature communications · 2026Article
- Resolving Conformational Heterogeneity in Intrinsically Disordered Proteins via Experimentally Guided Multi-Replica Simulations.bioRxiv : the preprint server for biology · 2026Article
- Elucidating HER2-directed chimeric antigen receptor (CAR) activation mechanism using homology modeling and all-atom molecular dynamics simulation.Computational and structural biotechnology journal · 2026Article
- Characterizing Structural and Kinetic Ensembles of Intrinsically Disordered Proteins Using Writhe.Journal of chemical theory and computation · 2025Article
- Monomer binding modes of small molecules that modulate the kinetics of hIAPP amyloid formation.bioRxiv : the preprint server for biology · 2025Article
- Ensemble Docking for Intrinsically Disordered Proteins.Journal of chemical information and modeling · 2025Article
- Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v1.0].Living journal of computational molecular science · 2025Article
- Covalent Adducts Formed by the Androgen Receptor Transactivation Domain and Small Molecule Drugs Remain Disordered.Journal of chemical information and modeling · 2025Article
- Ensemble docking for intrinsically disordered proteins.bioRxiv : the preprint server for biology · 2025Article
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5 authors.
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Abstract
Determining accurate atomic resolution conformational ensembles of intrinsically disordered proteins (IDPs) is extremely challenging. Molecular dynamics (MD) simulations provide atomistic conformational ensembles of IDPs, but their accuracy is highly dependent on the quality of physical models, or force fields, used. Here, we demonstrate how to determine accurate atomic resolution conformational ensembles of IDPs by integrating all-atom MD simulations with experimental data from nuclear magnetic resonance (NMR) spectroscopy and small-angle x-ray scattering (SAXS) with a simple, robust and fully automated maximum entropy reweighting procedure. We demonstrate that in favorable cases, where IDP ensembles obtained from different MD force fields are in reasonable initial agreement with experimental data, reweighted ensembles obtained with this approach converge to highly similar conformational distributions. The maximum entropy reweighting procedure presented here facilitates the integration of MD simulations with extensive experimental datasets and demonstrates progress towards the calculation of accurate, force-field independent conformational ensembles of IDPs at atomic resolution.
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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.