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List of works by Attilio V Vargiu

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Multidrug binding properties of the AcrB efflux pump characterized by molecular dynamics simulations.

scientific article
RND efflux pumps: structural information translated into function and inhibition mechanisms.

scientific article published on January 2013
AcrB drug-binding pocket substitution confers clinically relevant resistance and altered substrate specificity.

scientific article
Functional rotation of the transporter AcrB: insights into drug extrusion from simulations

scientific article (publication date: June 2010)
Effect of the F610A mutation on substrate extrusion in the AcrB transporter: explanation and rationale by molecular dynamics simulations

scientific article
Molecular basis for inhibition of AcrB multidrug efflux pump by novel and powerful pyranopyridine derivatives

scientific article published on 14 March 2016
Folding and self-assembly of the TatA translocation pore based on a charge zipper mechanism

scientific article
Recognition of imipenem and meropenem by the RND-transporter MexB studied by computer simulations

scientific article published on 12 November 2012
The Phe-Phe Motif for Peptide Self-Assembly in Nanomedicine

scientific article
Role of water during the extrusion of substrates by the efflux transporter AcrB.

scientific article
Some ligands enhance the efflux of other ligands by the Escherichia coli multidrug pump AcrB.

scientific article
Molecular Dynamics Computer Simulations of Multidrug RND Efflux Pumps

scientific article published on 03 March 2013
Aminoacyl β-naphthylamides as substrates and modulators of AcrB multidrug efflux pump

scientific article published on 19 January 2016
Dissociation of minor groove binders from DNA: insights from metadynamics simulations

scientific article
The hydrolysis mechanism of the anticancer ruthenium drugs NAMI-A and ICR investigated by DFT-PCM calculations

scientific article
Molecular Rationale behind the Differential Substrate Specificity of Bacterial RND Multi-Drug Transporters.

scientific article published on 14 August 2017
A novel dendrimeric peptide with antimicrobial properties: structure-function analysis of SB056.

scientific article
A Database of Force-Field Parameters, Dynamics, and Properties of Antimicrobial Compounds.

scientific article
Water-mediated interactions enable smooth substrate transport in a bacterial efflux pump

scientific article
Copper-1,10-phenanthroline complexes binding to DNA: structural predictions from molecular simulations

scientific article published in August 2009
Anthramycin-DNA binding explored by molecular simulations.

scientific article published on December 2006
Magnetic coupling between copper(II) ions mediated by hydrogen-bonded (neutral) water molecules

scientific article published in June 2009
Molecular mechanism of viral resistance to a potent non-nucleoside inhibitor unveiled by molecular simulations

scientific article
Different Molecular Mechanisms of Inhibition of Bovine Viral Diarrhea Virus and Hepatitis C Virus RNA-Dependent RNA Polymerases by a Novel Benzimidazole

scientific article published on May 15, 2013
Computational modelling of efflux pumps and their inhibitors.

scientific article published on February 2017
Computational study of correlated domain motions in the AcrB efflux transporter.

scientific article published on 5 January 2015
Effect of site-directed mutations in multidrug efflux pump AcrB examined by quantitative efflux assays

scientific article published on 24 October 2016
Molecular recognition of DNA by ligands: roughness and complexity of the free energy profile

scientific article published on October 2013
Structure–Activity Relationship Study of Hydroxycoumarins and Mushroom Tyrosinase

scientific article published on 11 August 2015
A New Critical Conformational Determinant of Multidrug Efflux by an MFS Transporter.

scientific article published on 9 March 2018
A kinetic Monte Carlo approach to investigate antibiotic translocation through bacterial porins

scientific article published on 21 February 2012
Atomistic-level portrayal of drug-DNA Interplay: a history of courtships and meetings revealed by molecular simulations

scientific article published on 05 August 2014
Editorial: Bad Bugs in the XXIst Century: Resistance Mediated by Multi-Drug Efflux Pumps in Gram-Negative Bacteria

scientific article published on 31 May 2016
Design of a hydrophobic tripeptide that self-assembles into amphiphilic superstructures forming a hydrogel biomaterial.

scientific article published on 21 March 2016
Holo-like and Druggable Protein Conformations from Enhanced Sampling of Binding Pocket Volume and Shape

scientific article published on 28 March 2019
Identification and characterization of carbapenem binding sites within the RND-transporter AcrB

scientific article published on 26 October 2018
Ru[(bpy)₂(dppz)]²⁺ and Rh[(bpy)₂(chrysi)]³⁺ targeting double strand DNA: the shape of the intercalating ligand tunes the free energy landscape of deintercalation

scientific article published on 23 July 2014
Detecting DNA mismatches with metallo-insertors: a molecular simulation study

scientific article published on 30 January 2012
HIV-1 Protease Dimerization Dynamics Reveals a Transient Druggable Binding Pocket at the Interface.

scientific article
Molecular Interactions of Cephalosporins with the Deep Binding Pocket of the RND Transporter AcrB

scientific article published on 28 May 2019
Computer simulations of the activity of RND efflux pumps

scientific article
Molecular Determinants of the Promiscuity of MexB and MexY Multidrug Transporters of Pseudomonas aeruginosa.

scientific article
Insights into the homo-oligomerization properties of N-terminal coiled-coil domain of Ebola virus VP35 protein.

scientific article published on 7 February 2018
Chlorpromazine and Amitriptyline Are Substrates and Inhibitors of the AcrB Multidrug Efflux Pump

scientific article published on 02 June 2020
Cryo-EM Structure and Molecular Dynamics Analysis of the Fluoroquinolone Resistant Mutant of the AcrB Transporter from Salmonella

scientific article published on 23 June 2020
Relevance of Ebola virus VP35 homo-dimerization on the type I interferon cascade inhibition

scientific article published on 01 January 2019
Pyridylpiperazine-based allosteric inhibitors of RND-type multidrug efflux pumps

scientific article published on 10 January 2022
Water-chloride and water-bromide hydrogen-bonded networks: influence of the nature of the halide ions on the stability of the supramolecular assemblies

scientific article published in July 2009
Toward the Prediction of Binding Events in Very Flexible, Allosteric, Multidomain Proteins

scientific article published on 5 February 2025
Coupling enhanced sampling of the apo-receptor with template-based ligand conformers selection: performance in pose prediction in the D3R Grand Challenge 4

scientific article published on 13 November 2019

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