SALAMI

SALAMI identifies structural similarities between protein chains by comparing their three-dimensional coordinates to detect structural homology independent of sequence information.

Key Features:

• Structure-Based Search: Uses the three-dimensional coordinates of a protein chain to search the Protein Data Bank (PDB) for structurally similar proteins.
• Sequence-Independent Analysis: Compares structures without relying on amino-acid sequence similarity, enabling detection of structural homologies not evident from sequence.
• Tolerance for Structural Variations: Employs an alignment method tolerant of large gaps and insertions, often producing slightly longer alignments than methods with stricter gap handling.

Scientific Applications:

• Functional Annotation: Infers possible functions of uncharacterized proteins by identifying structural similarity to proteins with known functions.
• Evolutionary Studies: Explores evolutionary relationships among proteins that have diverged at the sequence level but retain structural similarity.
• Drug Design and Discovery: Aids identification of potential targets or off-targets by revealing structural homologies relevant to pharmacological considerations.

Methodology:

Analyzes input three-dimensional coordinates and performs a comprehensive search of the PDB to identify structures with significant structural similarity, using an alignment method tolerant of large gaps and insertions and operating independently of sequence information.