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-Terán; Mireia 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

doi:10.1038/s41592-020-0884-y

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 (Lead / Corresponding author), Jana Selent (Lead / Corresponding author)

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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 language	English
Pages (from-to)	777-787
Number of pages	11
Journal	Nature Methods
Volume	17
Issue number	8
Early online date	13 Jul 2020
DOIs	https://doi.org/10.1038/s41592-020-0884-y
Publication status	Published - 1 Aug 2020

Keywords

Cell signalling
Membrane biophysics
Protein databases

ASJC Scopus subject areas

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

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10.1038/s41592-020-0884-y

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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

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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.",

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author = "Ismael Rodr{\'i}guez-Espigares and Mariona Torrens-Fontanals and Tiemann, {Johanna K. S.} and David Aranda-Garc{\'i}a and Ram{\'i}rez-Anguita, {Juan Manuel} and Stepniewski, {Tomasz Maciej} and Nathalie Worp and Alejandro Varela-Rial and Adri{\'a}n Morales-Pastor and Brian Medel-Lacruz and G{\'a}sp{\'a}r P{\'a}ndy-Szekeres and Eduardo Mayol and Toni Giorgino and Jens Carlsson and Xavier Deupi and Slawomir Filipek and Marta Filizola and G{\'o}mez-Tamayo, {Jos{\'e} Carlos} and Angel Gonzalez and Hugo Guti{\'e}rrez-de-Ter{\'a}n and Mireia Jim{\'e}nez-Ros{\'e}s and Willem Jespers and Jon Kapla and George Khelashvili and Peter Kolb and Dorota Latek and Maria Marti-Solano and Pierre Matricon and Matsoukas, {Minos Timotheos} and Przemyslaw Miszta and Mireia Olivella and Laura Perez-Benito and Davide Provasi and Santiago R{\'i}os and Torrecillas, {Iv{\'a}n R.} and Jessica Sallander and Agnieszka Sztyler and Silvana Vasile and Harel Weinstein and Ulrich Zachariae and Hildebrand, {Peter W.} and {De Fabritiis}, Gianni and Ferran Sanz and Gloriam, {David E.} and Arnau Cordomi and Ramon Guix{\`a}-Gonz{\'a}lez and Jana Selent",

year = "2020",

month = aug,

day = "1",

doi = "10.1038/s41592-020-0884-y",

language = "English",

volume = "17",

pages = "777--787",

journal = "Nature Methods",

issn = "1548-7091",

publisher = "Nature Research",

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Rodríguez-Espigares, I, Torrens-Fontanals, M, Tiemann, JKS, Aranda-García, D, Ramírez-Anguita, JM, Stepniewski, TM, 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, JC, Gonzalez, A, Gutiérrez-de-Terán, H, Jiménez-Rosés, M, Jespers, W, Kapla, J, Khelashvili, G, Kolb, P, Latek, D, Marti-Solano, M, Matricon, P, Matsoukas, MT, Miszta, P, Olivella, M, Perez-Benito, L, Provasi, D, Ríos, S, Torrecillas, IR, Sallander, J, Sztyler, A, Vasile, S, Weinstein, H, Zachariae, U, Hildebrand, PW, De Fabritiis, G, Sanz, F, Gloriam, DE, Cordomi, A, Guixà-González, R & Selent, J 2020, 'GPCRmd uncovers the dynamics of the 3D-GPCRome', Nature Methods, vol. 17, no. 8, pp. 777-787. https://doi.org/10.1038/s41592-020-0884-y

TY - JOUR

T1 - GPCRmd uncovers the dynamics of the 3D-GPCRome

AU - Rodríguez-Espigares, Ismael

AU - Torrens-Fontanals, Mariona

AU - Tiemann, Johanna K. S.

AU - Aranda-García, David

AU - Ramírez-Anguita, Juan Manuel

AU - Stepniewski, Tomasz Maciej

AU - Worp, Nathalie

AU - Varela-Rial, Alejandro

AU - Morales-Pastor, Adrián

AU - Medel-Lacruz, Brian

AU - Pándy-Szekeres, Gáspár

AU - Mayol, Eduardo

AU - Giorgino, Toni

AU - Carlsson, Jens

AU - Deupi, Xavier

AU - Filipek, Slawomir

AU - Filizola, Marta

AU - Gómez-Tamayo, José Carlos

AU - Gonzalez, Angel

AU - Gutiérrez-de-Terán, Hugo

AU - Jiménez-Rosés, Mireia

AU - Jespers, Willem

AU - Kapla, Jon

AU - Khelashvili, George

AU - Kolb, Peter

AU - Latek, Dorota

AU - Marti-Solano, Maria

AU - Matricon, Pierre

AU - Matsoukas, Minos Timotheos

AU - Miszta, Przemyslaw

AU - Olivella, Mireia

AU - Perez-Benito, Laura

AU - Provasi, Davide

AU - Ríos, Santiago

AU - Torrecillas, Iván R.

AU - Sallander, Jessica

AU - Sztyler, Agnieszka

AU - Vasile, Silvana

AU - Weinstein, Harel

AU - Zachariae, Ulrich

AU - Hildebrand, Peter W.

AU - De Fabritiis, Gianni

AU - Sanz, Ferran

AU - Gloriam, David E.

AU - Cordomi, Arnau

AU - Guixà-González, Ramon

AU - Selent, Jana

PY - 2020/8/1

Y1 - 2020/8/1

N2 - 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.

AB - 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.

KW - Cell signalling

KW - Membrane biophysics

KW - Protein databases

UR - http://www.scopus.com/inward/record.url?scp=85087806297&partnerID=8YFLogxK

U2 - 10.1038/s41592-020-0884-y

DO - 10.1038/s41592-020-0884-y

M3 - Article

C2 - 32661425

AN - SCOPUS:85087806297

SN - 1548-7091

VL - 17

SP - 777

EP - 787

JO - Nature Methods

JF - Nature Methods

IS - 8

ER -

GPCRmd uncovers the dynamics of the 3D-GPCRome

Abstract

Keywords

ASJC Scopus subject areas

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