Evidence map›Paper›PMID 33877632›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2021

Coarse-Grained Molecular Dynamics Simulations of Membrane Proteins: A Practical Guide.

William G Glass, Jonathan W Essex, Franca Fraternali, James Gebbie-Rayet, Irene Marzuoli, Marley L Samways, Philip C Biggin, Syma Khalid

Abstract read
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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Review
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

8 authors.

William G GlassDepartment of Biochemistry, University of Oxford, Oxford, UK.
Jonathan W EssexSchool of Chemistry, University of Southampton, Southampton, UK.
Franca FraternaliRandall Centre for Cell & Molecular Biophysics, Kings College London, London, UK.
James Gebbie-RayetScientific Computing Department, STFC Daresbury Laboratory, Warrington, UK.
Irene MarzuoliRandall Centre for Cell & Molecular Biophysics, Kings College London, London, UK.
Marley L SamwaysSchool of Chemistry, University of Southampton, Southampton, UK.
Philip C BigginDepartment of Biochemistry, University of Oxford, Oxford, UK. philip.biggin@bioch.ox.ac.uk.
Syma KhalidSchool of Chemistry, University of Southampton, Southampton, UK. s.khalid@soton.ac.uk.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Current computer architectures, coupled with state-of-the-art molecular dynamics simulation software, facilitate the in-depth study of large biomolecular systems at high levels of detail. However, biological phenomena take place at various time and length scales and as a result a multiscale approach must be adopted. One such approach is coarse-graining, where biochemical accuracy is sacrificed for computational efficiency. Here, we present a practical guide to setting up and carrying out coarse-grained molecular dynamics simulations.

Indexed as

Computational BiologyMembrane ProteinsModels, MolecularMolecular Dynamics SimulationSoftwareThermodynamicsMembrane ProteinsCoarse-grainedMembrane proteinMembranesMolecular dynamicsMolecular modelling

Identifiers

PMID33877632

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.