HerpesPPIs

This page displays LocalColabFold/AlphaFold Multimer predicted protein-protein dimer interactions in the herpesviruses HSV-1 strain 17 (UP000009294), HCMV strain Merlin (UP000000938), and KSHV strain GK18 (UP000000942).

All data is available for download at:

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.

Also, tell your friends about it. Thanks!

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, and click nodes to explore interactions. The dynamic table in the bottom right corner can be shown or hidden by clicking the triangular-shaped icon. Clicking on the links in the table will open the prediction website with scores and 3D models as well as submission links to Foldseek.

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 two viruses.

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.

Self-interactions are not rendered as self-loops on nodes as of now because this feature is still being developed for the Javascript library responsible for graph rendering. However, self-interactions show up in the dynamic table when clicking a node.

We are currently experiencing a bug that keeps us from hosting all HCMV predictions. We are working on a fix

Each virus type has been assigned a unique color:

HSV-1 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 LocalColaFold on the DESY compute cluster.

See also:

The network was created using the sigma.js and graphology Javascript libraries, which were developed by Alexis Jacomy and Guillaume Plique.
https://www.sigmajs.org/

This interface was developed by Robin Schäper

GNU General Public License v3.0

HerpesPPIs Copyright (C) 2024 Timothy K. Soh, Jens B. Bosse

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <https://www.gnu.org/licenses/>.