ArticleJournal of magnetic resonance (San Diego, Calif. : 1997)2016
Direct NOE simulation from long MD trajectories.
Article in Journal of magnetic resonance (San Diego, Calif. : 1997), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
What it found
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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
14 citing papers in PubMed.
- Computational toolbox for the analysis of protein-glycan interactions.Beilstein journal of organic chemistry · 2024Review
- AssignSLP_GUI, a software tool exploiting AI for NMR resonance assignment of sparsely labeled proteins.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2022Article
- Core packing of well-defined X-ray and NMR structures is the same.Protein science : a publication of the Protein Society · 2022Article
- Using molecular dynamics trajectories to predict nuclear spin relaxation behaviour in large spin systems.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2021Article
- Three-Dimensional Structures of Carbohydrates and Where to Find Them.International journal of molecular sciences · 2020Review
- Comparison of Methods for Bulk Automated Simulation of Glycosidic Bond Conformations.International journal of molecular sciences · 2020Article
- Specificity of Counterion Binding to a Conjugated Polyelectrolyte: A Combined Molecular Dynamics and NOESY Investigation.Macromolecules · 2020Article
- Enhancing NMR derived ensembles with kinetics on multiple timescales.Journal of biomolecular NMR · 2020Article
- Structural Aspects of the O-glycosylation Linkage in Glycopeptides via MD Simulations and Comparison with NMR Experiments.Chemphyschem : a European journal of chemical physics and physical chemistry · 2019Article
- NMR Resonance Assignment Methodology: Characterizing Large Sparsely Labeled Glycoproteins.Journal of molecular biology · 2019Article
- Molecular Dynamics Simulations of a Conformationally Mobile Peptide-Based Catalyst for Atroposelective Bromination.ACS catalysis · 2018Article
- Predicting the Structures of Glycans, Glycoproteins, and Their Complexes.Chemical reviews · 2018Review
- Oligosaccharide model of the vascular endothelial glycocalyx in physiological flow.Microfluidics and nanofluidics · 2018Article
- OThe Journal of biological chemistry · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
A software package, MD2NOE, is presented which calculates Nuclear Overhauser Effect (NOE) build-up curves directly from molecular dynamics (MD) trajectories. It differs from traditional approaches in that it calculates correlation functions directly from the trajectory instead of extracting inverse sixth power distance terms as an intermediate step in calculating NOEs. This is particularly important for molecules that sample conformational states on a timescale similar to molecular reorientation. The package is tested on sucrose and results are shown to differ in small but significant ways from those calculated using an inverse sixth power assumption. Results are also compared to experiment and found to be in reasonable agreement despite an expected underestimation of water viscosity by the water model selected.
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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.