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Carolina Estarellas and me had two sessions in the Summer school of Advanced Molecular Modelling: Biomolecules and Drug Design organised by the IQTC. We taught the principles behind molecular dynamics and gave the hands-on tutorial on how to set up a biological system using Ambertools.
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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.
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I have been granted access to PRACE DECI resources to study molecular mechanisms of antimicrobial resistance!
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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.