Super

Super performs rapid screening of the Protein Data Bank (PDB) to identify oligopeptide fragments that structurally align with a query structure for protein structural analyses.

Key Features:

• Rapid screening capability: Scans the Protein Data Bank (PDB) dataset of over 80,500 structures—approximately 40 million oligopeptide fragments—and executes typical queries in under a minute.
• Structural similarity measurement: Uses root-mean-square deviation (RMSD) as the structural similarity metric and accepts a user-specified RMSD threshold to filter matches.
• Efficient filtering mechanism: Computes mathematical bounds on RMSD values to pre-filter fragments, in some cases excluding over 99% of unrelated fragments before detailed comparison.

Scientific Applications:

• Protein structure analysis: Identifies well-fitting oligopeptide fragments to aid interpretation of folding patterns and conformational changes.
• Drug design and discovery: Finds peptide fragments that can mimic or disrupt specific protein interactions relevant to therapeutic development.
• Evolutionary studies: Compares structural similarities across proteins to inform evolutionary relationships and functional conservation.

Methodology:

Searches the PDB for oligopeptide fragments, computes RMSD between each fragment and the query with a user-specified threshold, and employs mathematical bounds on RMSD to pre-filter fragments (reducing over 99% in some cases); typical queries complete in under a minute.