Examples

Not sure what the MDsrv can do and how you can benefit from it? Check out our examples and get enthusiastic on how to present your work to reviewers, collaborators, the scientific community or simply to the public!


Simulations embedded into a website

Embedded simulations are a great opportunity to present your work along with the publication on your website. It also enriches websites which provide a selection of MD simulations (similar to structure viewer on the PDB) or which provide analysis of MD simulations.

More than a static video - as used here and on the home page, simulations can be embedded and automatically played within a web site. It can be interactively moved, scaled, centered and rotated.


Get more control! You can easily add additional functions (e.g. residue selection or coloring according to other analyses). Below, an embedded example with function button is shown. An html file with those functions can be downloaded and is further explained within the scripting section. Have also a look at the NGL gallery.





Simulation sessions served by MDsrv using the NGL GUI

You want to have more features to present the simulation (e.g. other representations, animation settings or trajectory processing)? By providing a simulation session served MDsrv using the NGL GUI, a manifold collection of options for visualization is available by default, offering greater flexibility and more features. Try out some of the prepared sessions below yourself:

  • Simulation of Rhodopsin with Gt peptide (3PQR): link #1
    200ns simulation of G-protein alpha-5 subunit peptide of transducin bound to active Opsin.

  • Spontaneous binding of cholesterol into A2A receptor: link #2
    Spontaneous binding of membrane cholesterol into A2A receptor. The simulation is deposed at the Hildebrand lab by using the MDsrv.

  • Coarse-Grained simulation of Bace1 helices: link #3
    Self-assembly of three Bace1 transmembrane helices and a DPPC lipid bilayer.

  • Simulation of a GPCR in complex with its G protein: link #4
    200ns of β2AR in complex with Gs-empty protein.

  • Coarse-Grained simulation of GPCR dimer: link #5
    Steer CG-MD simulation of GPCR dimer dissociation.

  • Simulation of a GPCR dimers in poly-lipid membranes: link #6
    PUFA-mediated GPCR oligomerization (Guixà-González et al. Sci. Rep. 2016 6:19839).

For information how to use the NGL GUI, e.g. to add simulation, change representations and adjust the playing settings, consult the "viewing simulation" documentation. Additionally, all script files used to generated the sessions can be downloaded here and is in general further explained here.


MDsrv used on other websites

GPCRmd: The GPCRmd is a consortium with the goal to establish a web platform including a database to allow storage of MD data, basic analysis of deposited MD trajectories (e.g. RMSD, ligand-receptor interaction, receptor dynamics) with the special focus on G-protein coupled receptors. It uses the MDsrv for on-line visualization and handling.

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