Evidence map›Paper›PMID 30259387›Full record

ArticleJournal of computer-aided molecular design2018

Parameterization of a coarse-grained model of cholesterol with point-dipole electrostatics.

P Siani, H Khandelia, M Orsi, L G Dias

Abstract read
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In one paragraph

Article in Journal of computer-aided molecular design, 2018. 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

4 authors.

P SianiDepartamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), Universidade de São Paulo (USP), Av. Bandeirantes, 3900, Ribeirão Preto, SP, 14040-901, Brazil. siani@usp.br.ORCID 0000-0002-1930-4579
H KhandeliaMEMPHYS-Center for Biomembrane Physics, Department of Physics and Chemistry, University of Southern Denmark, Odense, Denmark.
M OrsiDepartment of Applied Sciences, Faculty of Health and Applied Sciences, University of the West England (UWE Bristol), Bristol, UK.
L G DiasDepartamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), Universidade de São Paulo (USP), Av. Bandeirantes, 3900, Ribeirão Preto, SP, 14040-901, Brazil.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

We present a new coarse-grained (CG) model of cholesterol (CHOL) for the electrostatic-based ELBA force field. A distinguishing feature of our CHOL model is that the electrostatics is modeled by an explicit point dipole which interacts through an ideal vacuum permittivity. The CHOL model parameters were optimized in a systematic fashion, reproducing the electrostatic and nonpolar partitioning free energies of CHOL in lipid/water mixtures predicted by full-detailed atomistic molecular dynamics simulations. The CHOL model has been validated by comparison to structural, dynamic and thermodynamic properties with experimental and atomistic simulation reference data. The simulation of binary DPPC/cholesterol mixtures covering the relevant biological content of CHOL in mammalian membranes is shown to correctly predict the main lipid behavior as observed experimentally.

Indexed as

Molecular Dynamics SimulationCell MembraneCholesterolDiffusionLipid BilayersMolecular StructureStatic ElectricityThermodynamicsCholesterolLipid BilayersCholesterolCoarse-grainedDiffusionDPPCLipid bilayersMolecular dynamics

Identifiers

PMID30259387

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.