pocketZebra

pocketZebra identifies and ranks subfamily-specific binding sites within protein families to assess their functional significance and positions critical for selective ligand accommodation.

Key Features:

• Automated selection and classification: Automated selection and classification of subfamily-specific binding sites across diverse protein families.
• Bioinformatics and geometry-based approaches: Combines bioinformatics analyses and geometry-based structural approaches to detect and characterize binding sites.
• Novel scoring function: Implements a novel scoring function to assess binding sites by identifying positions in the protein structure critical for selective accommodation of ligands.
• Identification, ranking, and annotation: Identifies, ranks, and annotates binding sites based on their functional significance.
• Output formats: Produces outputs in annotated text format and as PyMol session files.

Scientific Applications:

• Structure–function analysis: Studying structure–function relationships and regulatory mechanisms in large protein superfamilies.
• Functional annotation: Classifying functionally important binding sites and annotating proteins of unknown function.
• Protein engineering: Supporting engineering of ligand-binding sites and modulation of allosteric regulation in enzymes.
• Drug discovery: Aiding identification of potential molecular targets and the development of selective inhibitors or effectors.

Methodology:

Combines bioinformatics analyses and geometry-based structural approaches with a novel scoring function to identify, rank, and annotate subfamily-specific binding sites by detecting positions critical for selective ligand accommodation.