Evidence map›Paper›PMID 42681251›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2026

Computer Simulations of Multidrug Efflux Pumps of the Resistance-Nodulation-Cell Division Superfamily.

Mohd Athar, Silvia Gervasoni, Giuliano Malloci, Paolo Ruggerone, Attilio V Vargiu

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Article in Methods in molecular biology (Clifton, N.J.), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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0citing papers in PubMed
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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

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3 · Its place in the literature

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0 citing papers in PubMed.

No citing paper in PubMed yet.

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

5 authors.

Mohd Athar *Physics Department, University of Cagliari, Monserrato, Italy.
Silvia Gervasoni *Physics Department, University of Cagliari, Monserrato, Italy.
Giuliano MallociPhysics Department, University of Cagliari, Monserrato, Italy.
Paolo RuggeronePhysics Department, University of Cagliari, Monserrato, Italy.
Attilio V VargiuPhysics Department, University of Cagliari, Monserrato, Italy. vargiu@dsf.unica.it.ORCID https://orcid.org/0000-0003-4013-8867

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Bacterial efflux pumps of the resistance-nodulation-cell division (RND) superfamily are major contributors to intrinsic and acquired multidrug resistance in Gram-negative bacteria. Structural and biochemical studies on AcrAB-TolC (E. coli) and MexAB-OprM (P. aeruginosa) pumps performed in the past decade have elucidated the molecular basis of allosteric transport by these complex machineries. Alongside these efforts, studies have also characterized the broad substrate specificity (polyspecificity) and molecular determinants that dictate the fate of substrates, inhibitors, and "avoiders" (molecules not actively transported) of RND transporters. Computational approaches have contributed to elucidating the structural and dynamic details of the functioning mechanisms of these transporters, including the interactions with substrates and inhibitors. In this chapter, we will discuss and illustrate several protocols developed in our lab on molecular docking, homology modeling, all-atom molecular dynamics simulations, and binding free energy estimation that have provided valuable insights into substrate recognition, extrusion mechanisms, optimization of efflux avoidance, and potential inhibition strategies.

Indexed as

Drug Resistance, Multiple, BacterialMembrane Transport ProteinsATP-Binding Cassette, Sub-Family C ProteinsBacterial Outer Membrane ProteinsComputer SimulationEscherichia coliEscherichia coli ProteinsMolecular Docking SimulationMolecular Dynamics SimulationATP-Binding Cassette, Sub-Family C ProteinsBacterial Outer Membrane ProteinsEscherichia coli ProteinsMembrane Transport ProteinsEfflux pumpsFragment-based drug designFree energy calculationsGram-negative bacteriaHomology modelingMD simulationsMembrane proteinsMM/GBSAMolecular dockingRND transporters

Identifiers

PMID42681251

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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.