ArticleIUCrJ2018
Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering.
Article in IUCrJ, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
18 citing papers in PubMed.
- Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v1.0].Living journal of computational molecular science · 2025Article
- An Unexpected Water Channel in the Light-Harvesting Complex of a Diatom: Implications for the Switch between Light Harvesting and Photoprotection.ACS physical chemistry Au · 2025Article
- Scaling and merging macromolecular diffuse scattering with mdx2.Acta crystallographica. Section D, Structural biology · 2024Article
- Functional protein dynamics in a crystal.Nature communications · 2024Article
- Functional Protein Dynamics in a Crystal.bioRxiv : the preprint server for biology · 2024Article
- Water Networks in Photosystem II Using Crystalline Molecular Dynamics Simulations and Room-Temperature XFEL Serial Crystallography.Journal of the American Chemical Society · 2023Article
- Robust total X-ray scattering workflow to study correlated motion of proteins in crystals.Nature communications · 2023Article
- Molecular Docking and Site-Directed Mutagenesis of GH49 Family Dextranase for the Preparation of High-Degree Polymerization Isomaltooligosaccharide.Biomolecules · 2023Article
- Molecular-dynamics simulation methods for macromolecular crystallography.Acta crystallographica. Section D, Structural biology · 2023Article
- Diffuse X-ray scattering from correlated motions in a protein crystal.Nature communications · 2020Article
- Advances in methods for atomic resolution macromolecular structure determination.F1000Research · 2020Review
- Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein.Structural dynamics (Melville, N.Y.) · 2019Article
- An introduction to classical molecular dynamics simulation for experimental scattering users.Journal of applied crystallography · 2019Article
- Biomolecular Solvation Structure Revealed by Molecular Dynamics Simulations.Journal of the American Chemical Society · 2019Article
- Article
- Bringing diffuse X-ray scattering into focus.Current opinion in structural biology · 2018Review
- Interactions that know no boundaries.IUCrJ · 2018Article
- Molecular Dynamics Simulations of Macromolecular Crystals.Wiley interdisciplinary reviews. Computational molecular scienceArticle
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structure to model disordered regions of the protein and local deviations of the average structure away from the crystal structure. Although it was anticipated that a simulation of longer duration might be required to achieve maximal agreement of the diffuse scattering calculation with the data using the supercell model, only a microsecond is required, the same as for the unit cell. Rigid protein motions only account for a minority fraction of the variation in atom positions from the simulation. The results indicate that protein crystal dynamics may be dominated by internal motions rather than packing interactions, and that MD simulations can be combined with Bragg and diffuse X-ray scattering to model the protein conformational ensemble.
Indexed as
Identifiers
What OpenQuestion holds
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.