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03/04/18

Thesis lecture of Ismael Rodríguez Espigares: "GPCRmd - A web platform for collection, visualization and analysis of molecular dynamics data for G protein-coupled receptors"

Next Wednesday, 4th April 2018 at 10h, Ismael Rodríguez Espigares, member of the GPCR drug discovery group of GRIB will defense his thesis "GPCRmd - A web platform for collection, visualization and analysis of molecular dynamics data for G protein-coupled receptors" at the Charles Darwin room, placed at the inner square of the PRBB building (Dr. Aiguader, 88).You are all invited to this event.

Abstract: 

In this thesis, we present GPCRmd, an online repository with a submission system and visualization platform specifically designed for storing and providing easy access to molecular dynamics (MD) data of G protein-coupled receptors (GPCRs). 

This database stores MD trajectories and necessary metadata (e.g. force-field, simulation software, integration time-step) for posterior analysis, ensuring data reproducibility and integrity. Importantly, we demonstrate the usefulness of the analysis tools implemented in GPCRmd in three case studies related to GPCR signaling bias, membrane-induced GPCR modulation and cross-receptor analysis of allosteric sodium binding.

The developed tools enabled us to detect important structural rearrangements in the initial phase of β-arrestin signaling of the δ-opioid receptor. In addition, we captured relevant molecular mechanisms responsible for cholesterol-induced modulation of the 5-HT2A receptor. Finally, we provide a comprehensive view of structural determinants that drive sodium binding across 31 different GPCRs.



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