Evidence map›Paper›PMID 39115764›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2024

Using AlphaFold2 and Molecular Dynamics Simulation to Model Protein Recognition.

Hiu Yan Wong, Kam-Bo Wong

Abstract read
PubMed Publisher
In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2024. 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

2 authors.

Hiu Yan WongSchool of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.
Kam-Bo WongSchool of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China. kbwong@cuhk.edu.hk.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

In this chapter, we predict the structure of the Arabidopsis receptor-homology-transmembrane-RING-H2 isoform 1 (RMR1) in complex with the C-terminal sorting determinant of cruciferin (CRU1) by AlphaFold2 using the ColabFold web interface and to perform molecular dynamics simulation to probe the dynamics of the predicted structures. Our results predict that the C-terminal carboxylate group of ctVSD of CRU1 is recognized by the conserved Arg89 of the cargo-binding loop of RMR1 and Arg468 of CRU1 by negative charge residues in the cargo-binding pocket of RMR1. The procedures described here are useful for modeling of other protein complexes.

Indexed as

ArabidopsisArabidopsis ProteinsMolecular Dynamics SimulationBinding SitesProtein BindingProtein ConformationSoftwareArabidopsis ProteinsMolecular modelingProtein foldingProtein interactionsStructure predictionVacuolar sorting

Identifiers

PMID39115764

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.