ATLIGATOR

ATLIGATOR analyzes structural protein interaction data to construct interaction atlases and facilitate the identification and design of protein–protein and protein–peptide interactions for molecular recognition studies.

Key Features:

• Interaction atlas construction: Builds interaction atlases from Protein Data Bank (PDB) structural data capturing detailed contacts, including interactions with single side chains.
• Pocket definition extraction: Extracts pocket definitions from atlases to identify recurrent interaction motifs and putative binding site geometries across proteins.
• Frequent-interaction identification and grafting: Identifies frequent residue-level interactions within pockets and enables grafting of these interactions onto new protein scaffolds to support design of novel binders.

Scientific Applications:

• Protein engineering: Informing redesign of protein interfaces by repurposing recurrent interaction motifs to alter binding specificity or affinity.
• Drug and binder design: Guiding the design of peptide or protein binders by mapping pocket interactions and transplanting favorable interaction patterns onto scaffolds.
• Molecular recognition studies: Characterizing residue-level interaction preferences and common pocket geometries to advance understanding of protein–protein and protein–peptide recognition.

Methodology:

Constructs interaction atlases from PDB structures, extracts pocket definitions, identifies frequent residue interactions within those pockets, and grafts identified interactions onto new protein scaffolds.