ProBiS

ProBiS detects protein binding sites by performing local structural alignments against the Protein Data Bank (PDB) to identify structurally similar binding sites for functional and interaction analysis.

Key Features:

• Local Structural Alignments: Performs local pairwise structural alignments to detect conserved binding site geometry.
• Parallelized Algorithms: Employs parallelized algorithms to accelerate comparisons between a query structure and the PDB, reducing computation time from hours to minutes.
• Pre-calculated Protein Similarity Profiles: Leverages the ProBiS-Database with pre-calculated similarity profiles for over 29,000 non-redundant protein structures to enable immediate comparisons.

Scientific Applications:

• Secondary Binding Site Identification: Detects secondary binding sites within proteins to support analysis of complex binding modes.
• Drug Discovery: Assists structure-based drug discovery by identifying conserved or similar binding sites across proteins.
• Enzyme Function Analysis: Aids enzyme function analysis by locating functionally relevant binding sites.
• Protein–Protein Interaction Exploration: Supports exploration of protein–protein interactions by finding structurally similar interfaces.

Methodology:

Performs local pairwise structural alignments of protein structures, uses parallelized algorithms for rapid comparisons against the Protein Data Bank (PDB), and leverages the ProBiS-Database of pre-calculated similarity profiles for over 29,000 non-redundant structures.