GPCRmd uncovers the dynamics of the 3D-GPCRome.
Ismael Rodríguez-EspigaresMariona Torrens-FontanalsJohanna K S TiemannDavid Aranda-GarcíaJuan Manuel Ramírez-AnguitaTomasz Maciej StepniewskiNathalie WorpAlejandro Varela-RialAdrián Morales-PastorBrian Medel-LacruzGáspár Pándy-SzekeresEduardo MayolToni GiorginoJens CarlssonXavier DeupiSlawomir FilipekMarta FilizolaJosé Carlos Gómez-TamayoAngel GonzalezHugo Gutiérrez-de-TeránMireia Jiménez-RosésWillem JespersJon KaplaGeorge KhelashvilliPeter KolbDorota LatekMaria Marti-SolanoPierre MatriconMinos-Timotheos MatsoukasPrzemyslaw MisztaMireia OlivellaLaura Perez-BenitoDavide ProvasiSantiago RíosIván R TorrecillasJessica SallanderAgnieszka SztylerSilvana VasileHarel WeinsteinUlrich ZachariaePeter W HildebrandGianni De FabritiisFerran SanzDavid E GloriamArnau CordomiRamon Guixà-GonzalézJana SelentPublished in: Nature methods (2020)
G-protein-coupled receptors (GPCRs) are involved in numerous physiological processes and are the most frequent targets of approved drugs. The explosion in the number of new three-dimensional (3D) molecular structures of GPCRs (3D-GPCRome) over the last decade has greatly advanced the mechanistic understanding and drug design opportunities for this protein family. Molecular dynamics (MD) simulations have become a widely established technique for exploring the conformational landscape of proteins at an atomic level. However, the analysis and visualization of MD simulations require efficient storage resources and specialized software. Here we present GPCRmd (http://gpcrmd.org/), an online platform that incorporates web-based visualization capabilities as well as a comprehensive and user-friendly analysis toolbox that allows scientists from different disciplines to visualize, analyze and share GPCR MD data. GPCRmd originates from a community-driven effort to create an open, interactive and standardized database of GPCR MD simulations.