Tools
03/04/18
Thesis lecture of Ismael RodrÃguez 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 RodrÃguez 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.
