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List of works by Paolo Ruggerone

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

scientific article

A kinetic Monte Carlo approach to investigate antibiotic translocation through bacterial porins

scientific article published on 21 February 2012

A novel dendrimeric peptide with antimicrobial properties: structure-function analysis of SB056.

scientific article

A scanning tunneling microscopy study of the GaAs(112) surfaces

AcrB drug-binding pocket substitution confers clinically relevant resistance and altered substrate specificity.

scientific article

Advanced computational methods in molecular medicine

scientific article published on 20 May 2012

Analysis of fast channel blockage: revealing substrate binding in the microsecond range

Anomalies in He atom scattering spectra of the H-covered Mo(110) and W(110) surfaces

Anthramycin-DNA binding explored by molecular simulations.

scientific article published on December 2006

Binding of novel azole-bridged dinuclear platinum(II) anticancer drugs to DNA: insights from hybrid QM/MM molecular dynamics simulations

scientific article published in March 2006

Breathing Motions of a Respiratory Protein Revealed by Molecular Dynamics Simulations

article

Bridging timescales and length scales: from macroscopic flux to the molecular mechanism of antibiotic diffusion through porins.

scientific article published on February 2010

CO escape from myoglobin with metadynamics simulations

scientific article published in May 2008

Chapter 13 Density-functional theory of epitaxial growth of metals

Combined helium-atom-scattering and molecular-dynamics study of aluminum surface-phonon anharmonicities and linewidths

article

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

Computer simulations of the activity of RND efflux pumps

scientific article

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

scientific article published in August 2009

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

Dissociation of minor groove binders from DNA: insights from metadynamics simulations

scientific article

Dynamics and structural assessment of open semiconductor surfaces: GaAs(110)

article

Dynamics of extensively reconstructed surfaces: Si(111) 2×1

scientific article published in Physical Review Letters

Effect of the F610A mutation on substrate extrusion in the AcrB transporter: explanation and rationale by molecular dynamics simulations.

scientific article

Electronic pseudocharge model for the Cu(111) longitudinal-surface-phonon anomaly observed by helium-atom scattering

article

Enhanced helium-atom scattering from longitudinal surface phonons in Cu(001)

scientific article published on 01 August 1993

Evidences of xenon-induced structural changes in the active site of cyano-metmyoglobins: a 1H NMR study

scientific article published in December 2008

Exploring binding properties of agonists interacting with a δ-opioid receptor

scientific article

Facilitated permeation of antibiotics across membrane channels--interaction of the quinolone moxifloxacin with the OmpF channel

scientific article

Folding and self-assembly of the TatA translocation pore based on a charge zipper mechanism

scientific article

Frustrated H-Induced Instability of Mo(110)

scientific article published in Physical Review Letters

Frustrated H-Induced Instability of Mo(110)

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

scientific article (publication date: June 2010)

Heme Proteins: The Role of Solvent in the Dynamics of Gates and Portals

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

Interaction of antibacterial compounds with RND efflux pumps in Pseudomonas aeruginosa

scientific article published on 8 July 2015

Intrinsic and extrinsic effects in surfaces: Acoustic-phonon softening of capped Si(111) surfaces

scientific article published on 01 October 1992

Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations

scientific article published on 6 April 2007

Investigating reaction pathways in rare events simulations of antibiotics diffusion through protein channels

scientific article published in November 2010

Lattice dynamics of GaAs(110) and Ge(111): 2 × 1

Molecular Dynamics Computer Simulations of Multidrug RND Efflux Pumps

scientific article published on 03 March 2013

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

scientific article published on 28 May 2019

Molecular Modeling of Multidrug Properties of Resistance Nodulation Division (RND) Transporters.

scientific article published in January 2018

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

scientific article published on 14 August 2017

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

scientific article published on 14 March 2016

Molecular basis for the different interactions of congeneric substrates with the polyspecific transporter AcrB

scientific article published on 08 May 2019

Molecular mechanism of MBX2319 inhibition of Escherichia coli AcrB multidrug efflux pump and comparison with other inhibitors

scientific article

Molecular mechanism of viral resistance to a potent non-nucleoside inhibitor unveiled by molecular simulations

scientific article

Molecular simulations reveal the mechanism and the determinants for ampicillin translocation through OmpF.

scientific article published in July 2010

Morphology, surface core-level shifts and surface energy of the faceted GaAs(112)A and (1̄1̄2̄)B surfaces

Parameterization of azole-bridged dinuclear platinum anticancer drugs via a QM/MM force matching procedure

scientific article published on 01 January 2008

Perturbed structural dynamics underlie inhibition and altered efflux of the multidrug resistance pump AcrB

scientific article published on 04 November 2020

Physical insights into permeation of and resistance to antibiotics in bacteria.

scientific article published on September 2008

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

scientific article published on January 2013

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

scientific article published on 12 November 2012

Relevance of Ebola virus VP35 homo-dimerization on the type I interferon cascade inhibition

scientific article published on 01 January 2019

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

scientific article

Scattering of Rare-Gas Atoms at a Metal Surface: Evidence of Anticorrugation of the Helium-Atom Potential Energy Surface and the Surface Electron Density

scientific article published in Physical Review Letters

Structural and Functional Characterization of a New Double Variant Haemoglobin (HbG-Philadelphia/Duarte α(2)β(2))

scientific article published on 29 November 2010

Structural and dynamical properties of the porins OmpF and OmpC: insights from molecular simulations.

scientific article published on 29 October 2010

Structure-function relationship in a variant hemoglobin: a combined computational-experimental approach.

scientific article published on 14 July 2006

Structure–Activity Relationship Study of Hydroxycoumarins and Mushroom Tyrosinase

scientific article published on 11 August 2015

Surface Phonons in Si(111) 2 × 1: Folding and Chain Effects of the Reconstruction

Surface lattice dynamics of the Pandey-reconstructed Si(111)-2 × 1: No pathologies in the experimental findings

Surface phonon dispersion curves in GaAs(110) and Ge(111)2 × 1: a critical comparison

article by Paolo Santini et al published January 1991 in Surface Science

Surface phonons in Si(111) + H(1×1)

scientific article published on 01 August 1988

Surface-phonon dispersion curves and the longitudinal resonance in Ag(001) observed by helium-atom scattering

scientific article published on 01 September 1994

The challenge of intracellular antibiotic accumulation, a function of fluoroquinolone influx versus bacterial efflux

scientific article published on 28 April 2020

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

scientific article

Theory of surface vibrations in epitaxial thin films

article

Toward screening for antibiotics with enhanced permeation properties through bacterial porins

scientific article published on August 2010

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

scientific article

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