Structural similarity networks across human herpesviruses.
HerpesClusters displays structural similarity networks across the nine human herpesviruses. Select Foldseek, HHblits, or unique subsets to compare alternative similarity definitions.
Click and drag to move around the stage, use the mouse wheel to zoom, and click nodes to inspect the linked AlphaFold prediction results. Edge thickness encodes structural similarity strength.
| Virus | Network colour |
|---|---|
| HSV-1 | #90ee90 |
| HSV-2 | #3cb371 |
| VZV | #008489 |
| HCMV | #cc0000 |
| HHV-6A | #ff0000 |
| HHV-6B | #ff6600 |
| HHV-7 | #ffa500 |
| EBV | #c4a0ff |
| KSHV | #8053b9 |
| Dataset | Evidence Type | Scope | Source |
|---|---|---|---|
| Foldseek structural similarity network | Structure search | All-against-all full-length herpesvirus protein pairs | Foldseek |
| HHblits profile similarity network | Profile search | HMM-HMM profile comparisons at the configured threshold | HH-suite / HHblits |
| Common / unique network subsets | Derived comparison | Common edges when both sources are selected, unique edges when one source and Unique are selected | Generated from the local HerpesClusters data processor |
If you use the structural similarity network, cite the HerpesFolds resource and the clustering/search methods relevant to your analysis.
Soh, T., & Bosse, J. (2024). HerpesFolds: A proteome-wide structural systems approach reveals insights into protein families and activities of all nine human herpesviruses. https://doi.org/10.1038/s41467-024-54668-2
The size (weight) of the connections encodes how significant the structural similarity is. A thicker connection indicates a more significant structural similarity than a thinner one. Thickness has been calculated as log10(E), where E is the expectation-value output. Foldseek estimates the E-value with the help of a neural network. The alignment type used in Foldseek was 3Di+AA Gotoh-Smith-Waterman.
Foldseek is developed by the Steinegger
lab:
van Kempen M, Kim S, Tumescheit C, Mirdita M, Soding J, and Steinegger M.
"Foldseek: fast and accurate protein structure search".
bioRxiv (2022) doi: 10.1101/2022.02.07.479398
HHblits is developed by the Soding Lab:
Remmert M, Biegert A, Hauser A, Soding J.
"HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment".
Nat Methods (2011) doi: 10.1038/nmeth.1818
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/
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 how related proteins across the nine human herpesviruses are. Clustering was performed with Foldseek and HHblits. Use the options above to explore interactions from different data sources.
Click and drag to move around the stage, use the mouse wheel to zoom, and click nodes to open a link and inspect the AlphaFold prediction results.
Each virus type has been assigned a unique color:
HSV-1 HSV-2 VZV HCMV HHV-6A HHV-6B HHV-7 EBV KSHV
The size (weight) of the connections encodes how significant the structural similarity is. A thicker connection indicates a more significant structural similarity than a thinner one. Thickness has been calculated as log10(E), where E is the expectation-value output. Foldseek estimates the E-value with the help of a neural network. The alignment type used in Foldseek was 3Di+AA Gotoh-Smith-Waterman.
Foldseek is developed by the Steinegger
lab:
van Kempen M, Kim S, Tumescheit C, Mirdita M, Soding J, and Steinegger M.
"Foldseek: fast and accurate protein structure search".
bioRxiv (2022) doi: 10.1101/2022.02.07.479398
HHblits is developed by the Soding Lab:
Remmert M, Biegert A, Hauser A, Soding J.
"HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment".
Nat Methods (2011) doi: 10.1038/nmeth.1818
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/