ProteinStructureFetch

This extension allows you to fetch protein structures from AlphaFold DB to explore them on the VRNetzer platform. This extension is built around the Python package vrprot. As vrprot uses ChimeraX it is mandatory to install it before using this extension.

Installation

1. Download and install the latest version of ChimeraX.
2. Add the ProteinStructureFetch directory to your VRNetzer backend directory. The directory should be located at "extensions/ProteinStructureFetch".
3. Before the line:

   python -m pip install -r requirements.txt
   

   add the following line to the VRNetzer backend's build and run script (Windows: buildandRUN.ps, Linux: linux_buildandrun.sh, Mac: mac_buildandrun.sh) :

   python -m pip install -r extensions/ProteinStructureFetch/requirements.txt
   

   It should now look something like this:

   python -m pip install -r extensions/ProteinStructureFetch/requirements.txt
   python -m pip install -r requirements.txt
   

Usage

Automatically fetch structures

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If you are in the VR of the VRNetzer and the network you are exploring is a PPI, you can select a node label. On the node panel, you'll see a second tab:

By selecting a protein structure in the dropdown menu, a fetching process is started in the background. If the structure has not yet been processed beforehand, the extension will fetch the structure from the AlphaFold DB and process it. This process takes some seconds. After the process is finished, the structure should rendered in the VR.

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API-References

Manually fetch structures

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To manually fetch a certain structure, you can navigate to:

http://localhost:5000/vrprot/fetch (Windows/Linux)

http://localhost:3000/vrprot/fetch (MacOS)

You define the protein structure you want to fetch by adding:

?id=<UniProtID_ID> to the URL.

For example, to fetch the structure with the UniProt ID P68871, you would navigate to:

http://localhost:5000/vrprot/fetch?id=P68871

Furthermore, you can define the mode in which the structure will be preprocessed in ChimarX by adding &mode=<MODE> to the URL.

To get a list of available modes you navigate to:

http://localhost:5000/vrprot/fetch?id=P68871&mode=help

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Fetch all structures of a project

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To fetch all structures of a project, you can navigate to:

http://localhost:5000/vrprot/project (Windows/Linux)

http://localhost:3000/vrprot/project (MacOS).

You define the project you want to fetch by adding:

/<PROJECT_NAME> to the URL.

For example, to fetch the project with the project name my_project, you would navigate to:

http://localhost:5000/vrprot/project/my_project

Here you can also define the mode as described above

For this to work, each node has to have a uniprot attribute which is a list of UniProt IDs. If a node has multiple UniProt IDs, all of them will be fetched and processed

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Fetch a list of structures

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To fetch a list of structures, you can navigate to:

http://localhost:5000/vrprot/list (Windows/Linux)

http://localhost:3000/vrprot/list (MacOS).

You define the list of structures by adding:

?ids=<UniProtID_1>,<UniProtID_2>,...,<UniProtID_N> to the URL.

For example, to fetch the structures with the UniProt IDs P68871 and P68872, you would navigate to:

http://localhost:5000/vrprot/list?ids=P68871,P68872

Here you can also define the mode as described above.

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Configuration

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The extension can be configured by editing the config.ini file in the ProteinStructureFetch directory. For every value in this config file there is a explanation provided. When this config file is not present, the extension will create a default config file. The coloring mode, AlphaFold DB version, and the overwrite mode can be changed in VR using the interactive panel which is added by this extension: