Explore predicted and experimentally validated protein-protein interactions across human herpesviruses. Select datasets, adjust confidence thresholds, and compare interaction networks.
Choose the datasets to include, then compare shared interactions or interactions specific to Group A. Confidence thresholds can be adjusted under Advanced Filters.
LocalColabFold / AlphaFold Multimer predicted protein-protein dimer interactions are integrated with experimental and curated source datasets for comparison.
| Virus | Strain | UniProt Proteome |
|---|---|---|
| HSV-1 | Strain 17 | UP000009294 |
| HCMV | Strain Merlin | UP000000938 |
| KSHV | Strain GK18 | UP000000942 |
| VZV | Strain Dumas | UP000008770 |
Use the selection board above to generate and compare networks. Shared interactions are present in every selected Group A dataset. Differential interactions are present in all Group A datasets but absent from Group B.
Click and drag to move around the network, use the mouse wheel to zoom, click nodes to explore proteins, and click edges to inspect interactions.
| Dataset | Evidence Type | Viruses | Weight Metric | Source |
|---|---|---|---|---|
| HerpesPPIs_Soh-2024 | Predicted (AF2) |
HSV-1
VZV
HCMV
KSHV
|
ipTM | Soh & Bosse 2024 |
| HSV-1_Cross-Link_Bogdanow-2025 | Cross-linking MS |
HSV-1
|
XLinks | Bogdanow et al. 2025 |
| HCMV_Cross-Link_Bogdanow-2023 | Cross-linking MS |
HCMV
|
XLinks | Bogdanow et al. 2023 |
| HVINT2_Duran-2019 | Curated database |
HSV-1
HCMV
EBV
|
Confidence Score | Duran et al. 2019 |
| IntAct | Curated database |
HSV-1
VZV
HCMV
EBV
|
MI Score | IntAct / EBI |
| MINT | Curated database |
HSV-1
VZV
HCMV
EBV
|
MI Score | MINT / UniRoma2 |
| HSV-1 LUCIA | Luciferase assay |
HSV-1
|
ratio / p-value | Zhang, Kraft & Soh |
This resource is the result of over 100,000 predicted models and several months of computing time. If you use HerpesPPIs in your work, please cite:
Soh, T., & Bosse, J. (2024). HerpesFolds: All-versus-all protein interaction network [Data set]. Zenodo. https://doi.org/10.5281/zenodo.12517508
Predictions were run with LocalColabFold on the DESY compute cluster.
Molecular visualization uses Mol* Viewer with JSmol as a fallback when WebGL is unavailable.
The interaction network is rendered using Cytoscape.js for graph visualization and analysis.
See also: Mirdita, M. et al. (2022). ColabFold: making protein folding accessible to all. GitHub
This software is licensed under the GNU General Public License v3.0.
You may redistribute and/or modify it under the terms of the GPL as published by the Free Software Foundation, version 3 or later. Read the full license text
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).
Data status: Interactions shown on this page were extracted from source databases on November 6, 2025.
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, click nodes to explore proteins and click on edges to explore interactions.
Use the selection board above to generate and compare networks. Select one or more datasets in "Include" (Group A). Common shows interactions present in every selected file of Group A (intersection). Unique A vs B shows interactions present in all files of A but in none of the files in B.
Reference for labels limits labels to the chosen base virus so that proteins from different datasets are mapped to the same identifiers; choose Auto to use the first file in A.
Each virus type has been assigned a unique color:
HSV-1 HSV-2 VZV HCMV HHV-6A HHV-6B HHV-7 EBV KSHV
This page uses David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K Burley, Jaroslav Koča, Alexander S Rose: Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures, Nucleic Acids Research, 2021; for molecular visualization, with JSmol as a fallback when WebGL is unavailable.
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/
GNU General Public License v3.0:
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/.
| Dataset | Weight Column |
|---|---|
| HerpesPPIs_Soh-2024: doi.org/10.1038/s41467-024-54668-2 | ipTM |
| HSV-1_Cross-Link_Bogdanow-2025: doi.org/10.1038/s41467-025-61618-z | XLinks |
| HCMV_Cross-Link_Bogdanow-2023: doi.org/10.1038/s41564-023-01433-8 | XLinks |
| HVINT2_Duran-2019: hvint2.topf-group.com • doi.org/10.1128/mSystems.00295-19 | Confidence Score |
| IntAct: ebi.ac.uk/intact • doi.org/10.1093/nar/gkab1006 | MI Score |
| MINT: mint.bio.uniroma2.it • doi.org/10.1093/nar/gkr930 | MI Score |
| HSV-1 LUCIA: • | ratio / p-value |