What is Erebus?
Erebus searches the entire Protein Data Bank (PDB) for protein structures containing a user-defined three-dimensional structural motif (substructure). Given a set of atoms and their 3D coordinates, it finds all proteins with a similar atomic arrangement using a rigid substructure search algorithm based on pairwise atom distances. Useful for identifying metal ion coordination scaffolds, small molecule binding pockets, and conserved structural motifs.
Workflow
Define a query structure (3–40 atoms in PDB format)
Set search parameters: matching precision, minimum weight, symmetric atoms
Erebus scans all ~105,000 PDB entries for matching substructures
Results are sorted by geometric similarity (weight) and RMSD
Download matching structures as PyMOL scripts or text files
Citation
Shirvanyants D, Alexandrova AN, Dokholyan NV.
“Rigid substructure search.”
Bioinformatics, 27(9): 1327–1329 (2011)
DOI: 10.1093/bioinformatics/btr129· PMID: 21460026· PMCID: PMC3138080