Segmentation of PhAge Endolysin Domains using Alphafold's PAE matrix

Description

SPAED is a tool for the segmentation (or identification) of phage endolysin domains. It applies hierarchical clustering to the predicted aligned error (PAE) file obtained from AlphaFold predictions to accurately delineate domains. SPAED was developed specifically with endolysins in mind, but feel free to try it on other types of modular proteins!

Usage

  1. Select your PAE file or zipped folder of PAE files (json format). If you have not, run AlphaFold to get it.
  2. Add multi-fasta or zipped folder of fasta files -> produce file of domain sequences.
  3. Add a pdb file or zipped folder of pdb files -> produce png or pymol file with 3D structure.
  4. Parameters can be adjusted in the "Advanced params" tab, but default parameters should be appropriate. Please read documentation first.

*All identifiers must match those in PAE files: PlySW4.json, PlySW4.pdb, >PlySW4.

Advanced params

Previous runs

Job ID Status Submitted (y/m/d EST) Download
*Jobs are saved for 3 days before being deleted. Please download results before then.

Citation

Boulay, A. et al. SPAED: Harnessing AlphaFold Output for Accurate Segmentation of Phage Endolysin Domains. 2025.04.25.650745 Preprint at https://doi.org/10.1101/2025.04.25.650745 (2025).

Contact

For any technical questions pertaining to the code or bugs please raise an issue on our GitHub page.