ESR1: Francho Nerín Fonz
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Host Organization
Cournia Lab Biomedical Research Foundation Academy of Athens Supervisor Dr. Zoe Cournia 
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Development of a computational methodology to detect allosteric pathways in proteins and application in drug discovery Recent years have seen numerous efforts to computationally model and engineer allosteric communication in proteins with a wide arrange of approaches, but these usually take advantage of a single or a specific set of descriptors that by themselves might not be able to capture or measure the entire complexity of the as-of-yet unknown allosteric mechanisms of proteins, and thus might not embody complete predictive power.
The aim of my project is to develop a computational method to detect allosterically important residues in proteins and apply it in computer-aided drug design (CADD), bringing together the different ways that allostery has been modelled in literature. This project intends to develop new ensemble Machine Learning (ML) and Deep Learning (DL) methodologies to predict allosteric residue hotspots in protein structures, making use of published, tried-and-tested benchmarking datasets for model training, and integrating the many existing sources of information as putative ML features, such as structural information, dynamics/conformational ensemble-derived features, or analyses coming from the graph theory-based modelling of the proteins. It will help to streamline the allosteric drug discovery process, from basic research to pharmaceutical drug development, and may offer essential insights into the mechanisms of protein allostery. |
Brief Scientific Bio
I got my BSc in Biotechnology from the University of Zaragoza, Spain, in 2020, where I completed a Bachelor’s final thesis dealing with Molecular Dynamics simulations for protein thermodynamics calculations. Previously, I had my first CADD experience working with a HER2 kinase inhibitor series during an Erasmus+ internship in Uppsala University, Sweden. I’ve always liked to think that it determined the rest of my career, and it was especially rewarding when my work became part of a publication in the Journal of Enzyme Inhibition and Medicinal Chemistry two years after, in 2021.
Afterwards, I decided to pursue a MSc in Bioinformatics at the Pompeu Fabra University in Barcelona, Spain. Between the 1st and 2nd year of the MSc, I also had my first experience in the private sector at the biotech/pharma start-up Nostrum Biodiscovery, in Barcelona, testing docking software for HTVS. Finally, during my Master’s final thesis, I developed a Python package for the calculation and analysis of allosteric communication networks in proteins, which notably prepared me for being an ESR now in ALLODD.
I got my BSc in Biotechnology from the University of Zaragoza, Spain, in 2020, where I completed a Bachelor’s final thesis dealing with Molecular Dynamics simulations for protein thermodynamics calculations. Previously, I had my first CADD experience working with a HER2 kinase inhibitor series during an Erasmus+ internship in Uppsala University, Sweden. I’ve always liked to think that it determined the rest of my career, and it was especially rewarding when my work became part of a publication in the Journal of Enzyme Inhibition and Medicinal Chemistry two years after, in 2021.
Afterwards, I decided to pursue a MSc in Bioinformatics at the Pompeu Fabra University in Barcelona, Spain. Between the 1st and 2nd year of the MSc, I also had my first experience in the private sector at the biotech/pharma start-up Nostrum Biodiscovery, in Barcelona, testing docking software for HTVS. Finally, during my Master’s final thesis, I developed a Python package for the calculation and analysis of allosteric communication networks in proteins, which notably prepared me for being an ESR now in ALLODD.
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This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 956314.
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