This page displays how structurally similar proteins across nine different types of herpes viruses are.

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 encode how significant the structural similarity is. A thicker connection indicates a more significant structural similarity than a thinner one. Thickness has been calculated as [math] -\log_{10}(E) [/math], where [math] E [/math] is the expectation-value output by foldseek. Foldseek estimates the [math] E [/math] -value with the help of a neural network. The alignment type used in foldseek was 3Di+AA Gotoh-Smith-Waterman.

More details can be found here:

https://github.com/steineggerlab/foldseek

Foldseek is developed by the Steinegger lab:
van Kempen M, Kim S, Tumescheit C, Mirdita M, Söding J, and Steinegger M. “Foldseek: fast and accurate protein structure search”.
bioRxiv (2022) doi: 10.1101/2022.02.07.479398

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

This interface was developed by Robin Schäper