Gallery

Video tutorial of Drug Discovery Tool (DDT) developed by Simone Aureli in the Limongelli Research Group (LRG) published on Bioinformatics 2019 doi: 10.1093/bioinformatics/btz543. DDT offers several powerful analysis tools helpful in drug design!

FMAP tutorial for the funnel-metadynamics approach published in Raniolo et Limongelli. Nature Protocol 2020.

Binding/unbinding events of benzamidine to trypsin under the action of funnel-metadynamics. Using a funnel restraint potential (right), several recrossing events between the bound and undound states of the ligand are possible, leading to a well-converged binding free energy surface and an accurate estimation of the aboslute protein-ligand binding free energy (Limongelli et al. PNAS 2013, 110:6358). Movie generated in the Limongelli Research Group (LRG).

The peculiar binding mechanism of Berberine to human telomeric G-quadruplex is disclosed with funnel-metadynamics calculations (Limongelli and co. PNAS 2017, 114:E2136). Movie generated for the Limongelli Research Group (LRG) by Federica Moraca.

Metadynamics simulation unveils the ligand binding mechanism to DNA G-quadruplex (Limongelli and co. NAR 2014, 42:5447). Movie generated in the Limongelli Research Group (LRG) by Francesco Saverio Di Leva.

Coarse-Grained Metadynamics reveals the dimerization mechanism of the transmembrane helices of the EGFR (Lelimousin, Limongelli & Sansom. JACS 2016, 138:10611).

Metadynamics simulation of the ligand binding to the Adenosine Deaminase (Limongelli et al. PNAS 2012, 109:1467). Movie generated in the Limongelli Research Group (LRG).

Movie generated in the Limongelli Research Group (LRG) by Stefano Raniolo.

Binding of benzamidine to trypsin through metadynamics simulations (Limongelli et al. PNAS 2013, 110:6358). Movie generated in the Limongelli Research Group (LRG).

Unfolding/folding process of the 3' end of the aptamer TBA under the action of metadynamics (Limongelli et al. Angew. Chem. Int. Ed. 2013, 52:2269). Movie generated in the Limongelli Research Group (LRG).

Unbinding of the coxib SC558 from COX-2 under metadynamics action (Limongelli et al. PNAS 2010, 107:5411). Movie generated in the Limongelli Research Group (LRG).

Adenosine binding to Adenosine A2A Receptor simulated using the Martini Coarse Grained force field and published in Souza et al. Nature Communications 2020.

Induced-fit and long-range allosteric effects investigated by funnel-metadynamics. More info at D'Annessa et al. J. Chem. Theory Comput. 2019, 15, 6368-6281.

Binding mode of 6 α-ethyl-3α,7α-dihydroxy-24-nor-5β-cholan-23-yl-23-triethylammonium sulfate (INT-767) to GP-BAR1 investigated by over 100 ns of molecular dynamics simulations (Limongelli and co. J Med Chem 2014, 57:937). Movie generated in the Limongelli Research Group (LRG) by Francesco Saverio Di Leva.