ASSAM

ASSAM identifies three-dimensional patterns of amino acid side chains in protein structures to reveal functional motifs that may be conserved despite sequence or fold divergence.

Key Features:

• Graph theoretical representation: Amino acid side chains are modeled as nodes in a labeled graph for spatial analysis.
• Pseudo-atom modeling: Each side chain is represented as a pseudo-atom that serves as a graph node.
• Distance-encoded edges: Inter-pseudo-atomic distances are encoded as labeled edges representing spatial relationships.
• 3D pattern input (PDB): Accepts a user-defined 3D pattern in Protein Data Bank (PDB) format defined by specific distances between side chains.
• Pattern search capability: Searches existing PDB structures for occurrences that match the user-defined 3D pattern.

Scientific Applications:

• Functional inference: Identification of spatially conserved side-chain patterns aids inference of potential functions for uncharacterized protein regions.
• Structural biology studies: Analysis of spatial organization and motifs within protein structures to investigate roles in biological processes.
• Comparative structural analysis: Comparison of 3D side-chain patterns across proteins to study evolutionary conservation and functional divergence.

Methodology:

Side chains are represented as pseudo-atoms and encoded as nodes in a labeled graph; inter-pseudo-atomic distances form labeled edges, and graph-theoretical matching is used to search PDB structures for pattern occurrences.