The GPCR molecular dynamics database

visualize · inspect · analyze

Examples: 5-hydroxytryptamine receptor 1b, 5ht1b_human, P28222, 4IAQ

Welcome to the online platform with web-based visualization capabilities and a comprehensive analysis toolbox that allows visualizing, inspecting, and analysing GPCR molecular dynamics.

Select a simulation to see the tool

Please note that not all the simulations have all the tools avilable. If you want to view a simulation with all tools check this example:
Adenosine receptor A2a in complex with xanthine amine congener (3REY)

Check the available simulations

Look into the family tree to find any simulated structure. The family tree helps you find the GPCR you are looking for. The GPCRs are classified by class and family. Finally, the different PDBs corresponding to each protein are displayed. Put your mouse in the PDB you are interested in and find out the different simulations.
There are more than 500 simulations available!

Receptor meta-analysis

Explore the receptor meta-analysis tool. Visualize the contact frequencies of all receptors in the database in a heatmap. You can select different simulations, interaction types, and cluster the receptors. Additionally, you can visualize the most frequent interactions of each cluster using different networks.
Check the tool!

Autoregulation of GPCR signalling through …

Sadler, Fredrik and Ma, Ning and Ritt, Michael and Sharma, Yatharth and Vaidehi, Nagarajan and …

The third intracellular loop (ICL3) of the G protein-coupled receptor (GPCR) fold is important for the signal transduction process downstream of receptor activation1-3. Despite this, the lack of a defined structure of ICL3, combined with its high sequence divergence among GPCRs, complicates characterization of its involvement in receptor signalling4. Previous …

Billesbølle, C.B., de March, C.A., van der Velden, W.J.C. et al.

Our sense of smell enables us to navigate a vast space of chemically diverse odour molecules. This task is accomplished by the combinatorial activation of approximately 400 odorant G protein-coupled receptors encoded in the human genome1-3. How odorants are recognized by odorant receptors remains unclear. Here we provide mechanistic insight …

Grimes, Jak and Koszegi, Zsombor and Lanoiselee, Yann and Miljus, Tamara and O'Brien, Shannon L. …

b-arrestin plays a key role in G protein-coupled receptor (GPCR) signaling and desensitization. Despite recent structural advances, the mechanisms that govern receptor-b-arrestin interactions at the plasma membrane of living cells remain elusive. Here, we combine single-molecule microscopy with molecular dynamics simulations to dissect the complex sequence of events involved in …

Marcus T. Hock, Abigail E. Teitgen, Kimberly J. McCabe, Sophia P. Hirakis, Gary A. Huber, …

2'-Deoxy-ATP (dATP), a naturally occurring near analog of ATP, is a well-documented myosin activator that has been shown to increase contractile force, improve pump function, and enhance lusitropy in the heart. Calcium transients in cardiomyocytes with elevated levels of dATP show faster calcium decay compared with cardiomyocytes with basal levels …

Manbir Sandhu, Aaron Cho, Ning Ma, Elizaveta Mukhaleva, Yoon Namkung, Sangbae Lee, Soumadwip Ghosh, John …

Recent studies have shown that G protein coupled receptors (GPCRs) show selective and promiscuous coupling to different Ga protein subfamilies and yet the mechanisms of the range of coupling preferences remain unclear. Here, we use Molecular Dynamics (MD) simulations on ten GPCR:G protein complexes and show that the location (spatial) …

Collaborative database

Our simulations have been computed and curated by our research team together with the collaboration of worldwide users that upload their own simulations.
Take a look at our dataset or upload your own simulation!