Molecular Modeling Lab


Efflux-mediated multi-drug resistance

  • 2023. Gervasoni et al., Molecular determinants of avoidance and inhibition of Pseudomonas aeruginosa MexB efflux pump, mBio, DOI: 10.1128/mbio.01403-23
  • 2023. Athar et al., Tripartite efflux pumps of the RND superfamily: what did we learn from computational studies?, Microbiology, DOI: 10.1099/mic.0.001307
  • 2022. Plé et al., Pyridylpiperazine-based allosteric inhibitors of RND-type multidrug efflux pumps, Nat. Commun., DOI: 10.1038/s41467-021-27726-2
  • 2021. Mehla et al., Predictive Rules of Efflux Inhibition and Avoidance in Pseudomonas aeruginosa, mBio, DOI: 10.1128/mBio.02785-20
  • 2020. Reading et al., Perturbed structural dynamics underlie inhibition and altered efflux of the multidrug resistance pump AcrB, Nature Communications, DOI: 10.1038/s41467-020-19397-2
  • 2020. Atzori et al., Molecular Interactions of Carbapenem Antibiotics with the Multidrug Efflux Transporter AcrB of Escherichia coli, International Journal of Molecular Sciences, DOI: 10.3390/ijms21030860
  • 2018. Vargiu et al., Water-mediated interactions enable smooth substrate transport in a bacterial efflux pump, Biochimica et Biophysica Acta, DOI: 10.1016/j.bbagen.2018.01.010
  • 2017. Ramaswamy et al., Molecular Rationale behind the Differential Substrate Specificity of Bacterial RND Multi-Drug Transporters, Scientific Reports, DOI: 10.1038/s41598-017-08747-8
  • 2016. Sjuts et al., Molecular basis for inhibition of AcrB multidrug efflux pump by novel and powerful pyranopyridine derivatives, Proceedings of the National Academy of Sciences of the United States of America, DOI: 10.1073/pnas.1602472113
  • 2015. Dreier et al., Interaction of antibacterial compounds with RND efflux pumps in Pseudomonas aeruginosa, Frontiers in Microbiology, DOI: 10.3389/fmicb.2015.00660

Self-assembly hydrogel peptides

  • 2021. Garcia et al., Nanoscale Assembly of Functional Peptides with Divergent Programming Elements, ACS Nano, DOI:
  • 2020. Kralj et al., Heterochirality and Halogenation Control Phe-Phe Hierarchical Assembly, ACS Nano, DOI:
  • 2018. Garcia et al., Chirality Effects on Peptide Self-Assembly Unraveled from Molecules to Materials, Chem, DOI: 10.1016/j.chempr.2018.05.016
  • 2016. Vargiu et al., Design of a hydrophobic tripeptide that self-assembles into amphiphilic superstructures forming a hydrogel biomaterial, Chemical Communications, DOI: 10.1039/c5cc10531e
  • 2015. Marchesan et al., The Phe-Phe Motif for Peptide Self-Assembly in Nanomedicine, Molecules, DOI: 10.3390/molecules201119658
  • 2015. Marchesan et al., Higher and lower supramolecular orders for the design of self-assembled heterochiral tripeptide hydrogel biomaterial, Journal of Materials Chemistry B, DOI: 10.1039/c5tb00858a

Characterization of physico-chemical properties of small molecules

  • 2022. Gervasoni et al., AB-DB: Force-Field parameters, MD trajectories, QM-based data, and Descriptors of Antimicrobials, DOI: 10.1038/s41597-022-01261-1
  • 2016. Malloci et al., Extracting Conformational Ensembles of Small Molecules from Molecular Dynamics Simulations: Ampicillin as a Test Case, DOI: 10.3390/computation4010005
  • 2015. Malloci et al., A Database of Force-Field Parameters, Dynamics, and Properties of Antimicrobial Compounds, Molecules, DOI: 10.3390/molecules200813997

Methods to improve the accuracy of in-silico molecular recognition

  • 2022. Basciu at al., No dance, no partner! A tale of receptor flexibility in docking and virtual screening, Annual Reports in Medicinal Chemistry, DOI: 10.1016/bs.armc.2022.08.006
  • 2020. Basciu at al., Coupling enhanced sampling of the apo-receptor with template-based ligand conformers selection: performance in pose prediction in the D3R Grand Challenge 4, Journal of Computer-Aided Molecular Design, DOI: 10.1007/s10822-019-00244-6
  • 2019. Basciu et al., Holo-like and Druggable Protein Conformations from Enhanced Sampling of Binding Pocket Volume and Shape, Journal of Chemical Information and Modeling, DOI: 10.1021/acs.jcim.8b00730
CONTACTS Giuliano Malloci Andrea Bosin Attilio Vittorio Vargiu Paolo Ruggerone