GPCRmd uncovers the dynamics of the 3D-GPCRome

Ismael Rodríguez-Espigares, Mariona Torrens-Fontanals, Johanna K. S. Tiemann, David Aranda-García, Juan Manuel Ramírez-Anguita, Tomasz Maciej Stepniewski, Nathalie Worp, Alejandro Varela-Rial, Adrián Morales-Pastor, Brian Medel-Lacruz, Gáspár Pándy-Szekeres, Eduardo Mayol, Toni Giorgino, Jens Carlsson, Xavier Deupi, Slawomir Filipek, Marta Filizola, José Carlos Gómez-Tamayo, Angel Gonzalez, Hugo Gutiérrez-de-TeránMireia Jiménez-Rosés, Willem Jespers, Jon Kapla, George Khelashvili, Peter Kolb, Dorota Latek, Maria Marti-Solano, Pierre Matricon, Minos Timotheos Matsoukas, Przemyslaw Miszta, Mireia Olivella, Laura Perez-Benito, Davide Provasi, Santiago Ríos, Iván R. Torrecillas, Jessica Sallander, Agnieszka Sztyler, Silvana Vasile, Harel Weinstein, Ulrich Zachariae, Peter W. Hildebrand, Gianni De Fabritiis, Ferran Sanz, David E. Gloriam, Arnau Cordomi, Ramon Guixà-González, Jana Selent

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)777-787
Number of pages11
JournalNature Methods
Volume17
Issue number8
Early online date13 Jul 2020
DOIs
Publication statusPublished - 1 Aug 2020

Keywords

  • Cell signalling
  • Membrane biophysics
  • Protein databases

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    Publisher Correction: GPCRmd uncovers the dynamics of the 3D-GPCRome

    Rodríguez-Espigares, I., Torrens-Fontanals, M., Tiemann, J. K. S., Aranda-García, D., Ramírez-Anguita, J. M., Stepniewski, T. M., Worp, N., Varela-Rial, A., Morales-Pastor, A., Medel-Lacruz, B., Pándy-Szekeres, G., Mayol, E., Giorgino, T., Carlsson, J., Deupi, X., Filipek, S., Filizola, M., Gómez-Tamayo, J. C., Gonzalez, A., Gutiérrez-de-Terán, H. & 27 others, Jiménez-Rosés, M., Jespers, W., Kapla, J., Khelashvili, G., Kolb, P., Latek, D., Marti-Solano, M., Matricon, P., Matsoukas, M. T., Miszta, P., Olivella, M., Perez-Benito, L., Provasi, D., Ríos, S., Torrecillas, I. R., Sallander, J., Sztyler, A., Vasile, S., Weinstein, H., Zachariae, U., Hildebrand, P. W., De Fabritiis, G., Sanz, F., Gloriam, D. E., Cordomi, A., Guixà-González, R. & Selent, J., 1 Aug 2020, In : Nature Methods. 17, 8, p. 861-862 2 p.

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  • Cite this

    Rodríguez-Espigares, I., Torrens-Fontanals, M., Tiemann, J. K. S., Aranda-García, D., Ramírez-Anguita, J. M., Stepniewski, T. M., Worp, N., Varela-Rial, A., Morales-Pastor, A., Medel-Lacruz, B., Pándy-Szekeres, G., Mayol, E., Giorgino, T., Carlsson, J., Deupi, X., Filipek, S., Filizola, M., Gómez-Tamayo, J. C., Gonzalez, A., ... Selent, J. (2020). GPCRmd uncovers the dynamics of the 3D-GPCRome. Nature Methods, 17(8), 777-787. https://doi.org/10.1038/s41592-020-0884-y