Evidence map›Paper›PMID 36042876›Full record

ArticleSTAR protocols2022

Protocol to study the oligomeric organization of single-span transmembrane peptides using molecular dynamics simulations.

Mauricio P Sica, Micaela V Kortsarz, Angelines A Morillas, Cristian R Smulski

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in STAR protocols, 2022. 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. 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.

Mauricio P SicaMedical Physics Department, Centro Atómico Bariloche, Comisión Nacional de Energía Atómica (CNEA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. E. Bustillo 9500, San Carlos de Bariloche, Río Negro R8402AGP, Argentina.
Micaela V KortsarzMedical Physics Department, Centro Atómico Bariloche, Comisión Nacional de Energía Atómica (CNEA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. E. Bustillo 9500, San Carlos de Bariloche, Río Negro R8402AGP, Argentina.
Angelines A MorillasCentro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Av. Complutense 40, 28040 Madrid, España.
Cristian R SmulskiMedical Physics Department, Centro Atómico Bariloche, Comisión Nacional de Energía Atómica (CNEA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. E. Bustillo 9500, San Carlos de Bariloche, Río Negro R8402AGP, Argentina. Electronic address: cristian.smulski@cab.cnea.gov.ar.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Herein, you will find detailed information for the preparation of a coarse-grained array of peptides embedded in a lipid membrane. It contains all the steps to set up and run a molecular dynamic simulation using a coarse-grained approach. We provide analytical tools and scripts for generating a residue-level contact matrix between multiple peptides, as well as geometric analysis of arrangements between multiple peptides. This protocol was designed to study the organization of transmembrane peptides in an unbiased manner using computational approaches. For complete details on the use and execution of this protocol, please refer to Smulski et al. (2022).

Indexed as

Molecular Dynamics SimulationPeptidesPeptidesBioinformaticsCell MembraneProtein BiochemistryStructural Biology

Identifiers

PMID36042876
PMCPMC9420530

What OpenQuestion holds

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Registered trials

None linked

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.