2020
DOI: 10.1038/s41592-020-0884-y
|View full text |Cite|
|
Sign up to set email alerts
|

GPCRmd uncovers the dynamics of the 3D-GPCRome

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 3D molecular structures of GPCRs (3D-GPCRome) during 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 to explore the conformational landscape of proteins at an atomic level. However, the ana… Show more

Help me understand this report
View preprint versions

Search citation statements

Order By: Relevance

Paper Sections

Select...
2
1
1
1

Citation Types

1
86
0

Year Published

2020
2020
2023
2023

Publication Types

Select...
7
2

Relationship

3
6

Authors

Journals

citations
Cited by 96 publications
(87 citation statements)
references
References 42 publications
1
86
0
Order By: Relevance
“…Three-dimensional structures of GPCRs reveal allosteric binding sites spanning extracellular, transmembrane, and intracellular regions; identification of novel allosteric sites in GPCRs can provide alternative options for drug discovery 39 . To demonstrate the use of BiteNet in spatiotemporal identification of GPCR binding sites we analyzed molecular dynamics trajectories of the human adenosine A2A receptor (A2A) retrieved from the GPCRmd repository 40 .…”
Section: Resultsmentioning
confidence: 99%
“…Three-dimensional structures of GPCRs reveal allosteric binding sites spanning extracellular, transmembrane, and intracellular regions; identification of novel allosteric sites in GPCRs can provide alternative options for drug discovery 39 . To demonstrate the use of BiteNet in spatiotemporal identification of GPCR binding sites we analyzed molecular dynamics trajectories of the human adenosine A2A receptor (A2A) retrieved from the GPCRmd repository 40 .…”
Section: Resultsmentioning
confidence: 99%
“…Such information would help us better understand GPCR physiology and inform the design of molecules with a specific signaling profile [ 52 ]. A valuable resource of ligand binding dynamics is found in the recently established GPCRmd server [ 53 ], which provides intuitive visualization and analysis tools currently covering 70% of crystallized receptor subtypes ( Figure 2 ).…”
Section: Complementing Static Datamentioning
confidence: 99%
“…To analyze them, more specialized tools have been developed, such as the python module GetContacts [ 141 ]. A good example of the capabilities of this module can be found in the Receptor Meta-analysis web tool ( ) included in the GPCRmd platform [ 53 ]. This tool analyzes and compares different types of non-covalent interactions obtained from a large GPCR simulation dataset using GetContacts scripts, and displays them into a series of interactive plots ( Figure 5 ).…”
Section: MD Analysis—extracting Data From the Simulationsmentioning
confidence: 99%
“…Consequently, the call for public availability and conservation of data has extended to molecular dynamics (MD) simulation trajectories of biomolecules, [20][21][22] and the discussion on how and by whom such databanks for dynamic structures would be set up is currently active. [23][24][25][26] While there are currently no general MD databanks in operation, individual databanks are accepting contributions on nucleic acid, 27 protein/DNA/RNA, 28 cyclodextrin, 29 G-protein-coupled receptor, 30 and lipid bilayer 31 simulations.…”
Section: Introductionmentioning
confidence: 99%