This page displays LocalColabFold/AlphaFold Multimer predicted protein-protein dimer interactions in the herpesviruses HSV-1 strain 17 (UP000009294), HCMV strain Merlin (UP000000938), KSHV strain GK18 (UP000000942) and VZV strain Dumas (UP000008770).
Soh, T., & Bosse, J. (2024). HerpesFolds: All-versus-all protein interaction network [Data set]. Zenodo.
https://doi.org/10.5281/zenodo.12517508
Please cite this resource if you find it useful. It results from over 100,000 predicted models and several months of computing.
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Keep in mind that some proteins, such as gB, will need to form high-order oligomers to function. Therefore, the dimeric predictions displayed here might inform on interfaces but they might not represent functional units.
Click and drag to move around, use the mouse wheel to zoom, click nodes to explore proteins and click on edges to explore interactions.
Clicking on the buttons selects the virus interactome. When more than one button is selected, the conserved interactions between the viruses are displayed. The unique button displays interactions uniquely found in one virus or interactions uniquely conserved between more viruses.
The table on the right lists all interactions. Clicking on the column headers will sort the table. Clicking on a node filters the table to show only interactions with that protein. Clicking in the background of the graph deselects the protein and all interactions are shown again. The links in the protein source and target columns will open the prediction website for the monomer with the scores and 3D models. The link in the ipTM column will open the PPI website with the scores and predicted 3D models.
The size (weight) of the connections encodes how well an interaction was predicted by AlphaFold 2. A thicker connection indicates a more likely interaction than a thinner one. Thickness is calculated from AlphaFold Multimer’s ipTM value. Only interactions with an ipTM value greater than 0.47 are shown. The ipTM values have been normalized and scaled from a 0.47-1.00 to a -1-8 scale for easier visual interpretation.
HSV-1 VZV HCMV KSHV
This is a project in cooperation with the Topf lab at CSSB.
The predictions are visualized using 3Dmol.js:
Predictions were run with LocalColabFold on the DESY compute cluster.
See also:
The network was created using cytoscape.js, a Graph theory library for visualization and analysis, which was developed by Franz M, Lopes CT, Huck G, Dong Y, Sumer O, Bader GD at the University of Toronto https://js.cytoscape.org/
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