Erebus

Erebus identifies protein binding-site substructures in the Protein Data Bank (PDB) to support molecular docking, de novo drug design, structure identification, and comparative analysis of functional sites.

Key Features:

• Substructure search: Defines query substructures based on a user-specified set of atoms to locate binding scaffolds for small molecules and metal ions within the PDB.
• Atom matching criteria: Requires matched atoms to have identical atom names, belong to the same amino acids, and be separated by equivalent distances within a specified tolerance.
• Accuracy measurement: Assesses match accuracy using root-mean-square deviation (RMSD) or normal weight with given variance.
• Rigid scaffold handling: Supports reliable identification of rigid binding scaffolds relevant to drug and metal ion interactions.

Scientific Applications:

• Molecular docking and drug design: Identifies potential binding sites and scaffolds to inform de novo drug design and optimization of small-molecule interactions.
• Structure identification: Discovers proteins with similar binding-site substructures to aid functional annotation.
• Functional site comparison: Enables comparative analysis of binding sites across proteins to study function and evolutionary relationships.

Methodology:

Scans the entire PDB for user-defined atom-based substructure queries, matches atoms by identical names and amino acids with distance tolerances, and evaluates matches using RMSD or normal weight with given variance while handling rigid binding scaffolds.