ArticleActa crystallographica. Section D, Structural biology2021
Improving sampling of crystallographic disorder in ensemble refinement.
Article in Acta crystallographica. Section D, Structural biology, 2021. 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.
- From possibility to precision in macromolecular ensemble prediction.Nature methods · 2026Article
- Dynamical network analysis reveals long-range residue couplings at the pMHC interface underlying enhanced immunogenicity.NPJ systems biology and applications · 2026Article
- Multi-Temperature Crystallography of S-Adenosylmethionine Decarboxylase Observes Dynamic Loop Motions.Biomolecules · 2025Article
- Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v1.0].Living journal of computational molecular science · 2025Article
- A snapshot love story: what serial crystallography has done and will do for us.Acta crystallographica. Section D, Structural biology · 2024Review
- Cryo2RT: a high-throughput method for room-temperature macromolecular crystallography from cryo-cooled crystals.Acta crystallographica. Section D, Structural biology · 2024Article
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- Article
- Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM.bioRxiv : the preprint server for biology · 2024Article
- Functional protein dynamics in a crystal.Nature communications · 2024Article
- Functional Protein Dynamics in a Crystal.bioRxiv : the preprint server for biology · 2024Article
- Synergism between x-ray crystallography and NMR residual dipolar couplings in characterizing protein dynamics.Structural dynamics (Melville, N.Y.) · 2023Article
- FLEXR: automated multi-conformer model building using electron-density map sampling.Acta crystallographica. Section D, Structural biology · 2023Article
- Obtaining anomalous and ensemble information from protein crystals from 220 K up to physiological temperatures.Acta crystallographica. Section D, Structural biology · 2023Article
- Molecular-dynamics simulation methods for macromolecular crystallography.Acta crystallographica. Section D, Structural biology · 2023Article
- Refinement of multiconformer ensemble models from multi-temperature X-ray diffraction data.Methods in enzymology · 2023Article
- Error estimates in atom coordinates and B factors in macromolecular crystallography.Current research in structural biology · 2023Review
- Mechanistic basis of GPCR activation explored by ensemble refinement of crystallographic structures.Protein science : a publication of the Protein Society · 2022Article
- Article
- Ten things I `hate' about refinement.Acta crystallographica. Section D, Structural biology · 2021Article
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4 authors.
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Abstract
Ensemble refinement, the application of molecular dynamics to crystallographic refinement, explicitly models the disorder inherent in macromolecular structures. These ensemble models have been shown to produce more accurate structures than traditional single-model structures. However, suboptimal sampling of the molecular-dynamics simulation and modelling of crystallographic disorder has limited the utility of the method, and can lead to unphysical and strained models. Here, two improvements to the ensemble refinement method implemented within Phenix are presented: DEN restraints, which guide the local sampling of conformations and allow a more robust exploration of local conformational landscapes, and ECHT disorder models, which allow the selection of more physically meaningful and effective disorder models for parameterizing the continuous disorder components within a crystal. These improvements lead to more consistent and physically interpretable simulations of macromolecules in crystals, and allow structural heterogeneity and disorder to be systematically explored on different scales. The new approach is demonstrated on several case studies and the SARS-CoV-2 main protease, and demonstrates how the choice of disorder model affects the type of disorder that is sampled by the restrained molecular-dynamics simulation.
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