Evidence map›Paper›PMID 33445107›Full record

ArticleJournal of magnetic resonance (San Diego, Calif. : 1997)2021

Using molecular dynamics trajectories to predict nuclear spin relaxation behaviour in large spin systems.

Ilya Kuprov, Laura C Morris, John N Glushka, James H Prestegard

Abstract read
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In one paragraph

Article in Journal of magnetic resonance (San Diego, Calif. : 1997), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed.

  1. Neural net analysis of NMR spectra from strongly-coupled spin systems.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2024
    Article
  2. Review
  3. Article
  4. Review
  5. Stochastic Modelling ofMolecules (Basel, Switzerland) · 2021
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors.

Ilya KuprovSchool of Chemistry, University of Southampton, Southampton, UK.
Laura C MorrisComplex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States.
John N GlushkaComplex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States.
James H PrestegardComplex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States. Electronic address: jpresteg@uga.edu.

Funding

Sparse NMR Labeling Approach to Glycoprotein Structure and FunctionR01GM134335 · NIGMS · UNIVERSITY OF GEORGIA · PI PRESTEGARD, JAMES H. · 2019 to 2022
$1.2M
NIGMS NIH HHS R01 GM134335
6 · The paper itself

Abstract

Molecular dynamics (MD) trajectories provide useful insights into molecular structure and dynamics. However, questions persist about the quantitative accuracy of those insights. Experimental NMR spin relaxation rates can be used as tests, but only if relaxation superoperators can be efficiently computed from MD trajectories - no mean feat for the quantum Liouville space formalism where matrix dimensions quadruple with each added spin 1/2. Here we report a module for the Spinach software framework that computes Bloch-Redfield-Wangsness relaxation superoperators (including non-secular terms and cross-correlations) from MD trajectories. Predicted initial slopes of nuclear Overhauser effects for sucrose trajectories using advanced water models and a force field optimised for glycans are within 25% of experimental values.

Indexed as

Molecular Dynamics SimulationNuclear Magnetic Resonance, BiomolecularPredictive Value of TestsSucroseWaterSucroseWaterGlycan force fieldsMolecular dynamicsSpin relaxationWater models

Identifiers

PMID33445107
PMCPMC7873838

What OpenQuestion holds

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Registered trials

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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.