HerpesClusters

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/