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GPCRmd uncovers the dynamics of the 3D-GPCRome.

Authors :
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
R Torrecillas I
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
Source :
Nature methods [Nat Methods] 2020 Aug; Vol. 17 (8), pp. 777-787. Date of Electronic Publication: 2020 Jul 13.
Publication Year :
2020

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.

Details

Language :
English
ISSN :
1548-7105
Volume :
17
Issue :
8
Database :
MEDLINE
Journal :
Nature methods
Publication Type :
Academic Journal
Accession number :
32661425
Full Text :
https://doi.org/10.1038/s41592-020-0884-y