Protemot

Protemot predicts protein binding sites by matching geometrical tertiary substructures of query proteins to structural templates automatically extracted from crystal structures of protein–ligand complexes in the Protein Data Bank (PDB).

Key Features:

• Automatic Template Extraction: Automatically extracts structural templates from crystal structures of protein–ligand complexes in the PDB.
• Template Library: Maintains a comprehensive, dynamically updated template library built from automatically extracted PDB templates.
• Geometrical Tertiary-Substructure Analysis: Employs geometrical analysis of protein tertiary substructures to identify structural motifs relevant to ligand binding.
• Tertiary Substructure Matching: Matches tertiary substructures on the contour of the query protein against templates in the library.
• Efficient Analysis Mechanism: Applies a rapid analysis mechanism to accelerate matching and prediction despite library growth.
• Demonstrated Prediction Performance: Experimental evaluations report superior prediction power compared to servers using manually curated, limited template libraries.

Scientific Applications:

• Binding Site Identification: Identification of potential protein binding sites for structural and functional studies.
• Protein–Ligand Interaction Analysis: Exploration of protein–ligand interactions using structurally derived template matches.
• Drug Design and Therapeutic Development: Support for drug design efforts by locating candidate ligand-binding regions on target proteins.
• Structural Bioinformatics Research: Use in structural biology and computational biology studies that require up-to-date template-based binding-site predictions.

Methodology:

Automatically extract structural templates from PDB entries of crystal protein–ligand complexes; perform geometrical analysis of protein tertiary substructures; match tertiary substructures on the contour of the query protein to templates in the library; and apply a rapid analysis mechanism to generate binding-site predictions.