Salomé Llabrés Prat

Salomé Llabrés Prat

Juan de la Cierva Researcher at the CBCG and CBDD groups at University of Barcelona.

Granted a PRACE Distributed European Computing Initiative (DECI) Call

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I have been granted access to PRACE DECI resources to study molecular mechanisms of antimicrobial resistance!

We will use the brand new Snellius supercomputer to shed light on the molecular mechanism of a efflux pump of E. coli using molecular dynamics simulations. Unravelling the mechanism that underpins its function will help us understand how this complex machinery works and how to inhibit it with small molecules. Efflux Pump Inhibitors have the potential to restore the effectivity of antibiotic treatments on bacterial strains that have become resistant, and therefore help tackle the unfolding antimicrobial resistance crisis.

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My postdoctoral work is finally published in Chemical Science.

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My postdoctoral work on the selectivity of a drug-like small molecules on the oncoprotein MDM2 is finally out in Chemical Science. While I was a PDRA at the group of Dr Julien Michel at the University of Edinburgh, we explored the molecular determinants that guide the binding of Nutlin-3a and AMG-7209 to MDM2, which involves the disorder-to-order transition of the intrinsically disordered N-terminal region of MDM2. Moreover, we developed a protocol able to accurately estimate the binding affinities of these ligands using complete thermodynamic analysis that featured adaptive absolute alchemical free energy of binding calculations with enhanced-sampling molecular dynamics simulations.

Best Practice Guide for Biomolecular QM/MM simulations with CP2K

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As part of my work in the BioExcel-2 project at the EPCC, I co-wrote a best practice guide on how to perform QM/MM simulations of biomolecules using CP2K. We provided an overview of the main steps in setting up and running a QM/MM simulation in CP2K. We cover steps starting from preparing your system to running a production QM/MM run. This BPG is designed to be read from the point of view of beginner users.