PAST

Polypeptide Angles Suffix Tree (PAST) performs sequence-independent structural queries of Protein Data Bank (PDB) polypeptide chains using a generalized suffix tree representation of backbone geometry.

Key Features:

• Translation- and Rotation-Invariant Backbone Encoding: Represents protein backbone geometry in a spatially invariant form to enable orientation-independent three-dimensional structure matching.
• Generalized Suffix Tree–Based Structural Search: Adapts the generalized suffix tree algorithm to identify frequent common substructures and short structural motifs without sequence constraints or dataset prefiltering.

Scientific Applications:

• Protein Structural Motif Discovery: Detects recurrent three-dimensional substructures and functional motifs in PDB entries, including short protein fragments.

Methodology:

PAST encodes protein backbone angles into a translation- and rotation-invariant representation and applies a generalized suffix tree algorithm to perform exhaustive, sequence-independent structural pattern searches across PDB polypeptide chains.