SITEHOUND-web

SITEHOUND-web identifies potential ligand binding sites within protein structures by detecting regions favorable for interactions with probe molecules to support protein–ligand interaction analysis.

Key Features:

• SITEHOUND program: Uses the SITEHOUND program to analyze protein structures.
• PDB input: Accepts protein structures submitted in PDB format.
• Carbon probe: Employs a carbon probe to identify binding sites suitable for drug-like molecules.
• Phosphate probe: Employs a phosphate probe to pinpoint sites that preferentially bind phosphorylated ligands such as ATP and phosphopeptides.
• Binding-site detection: Detects regions on proteins that exhibit favorable interactions with specific probe molecules indicative of potential ligand binding sites.
• 3D visualization: Provides a 3D representation of the protein structure and identified putative binding sites via the Jmol Java applet.
• Output files: Produces downloadable data files for further offline analysis.

Scientific Applications:

• Structural biology: Mapping putative ligand binding sites on protein structures to inform structural interpretation.
• Drug discovery: Identifying candidate sites for drug-like molecules to aid lead identification and design.
• Phosphorylation-related studies: Locating sites that bind phosphorylated ligands such as ATP and phosphopeptides to study phosphorylation-mediated interactions.
• Experimental planning: Prioritizing candidate binding regions to inform experimental design and therapeutic development.

Methodology:

Analyzes PDB-format protein structures with the SITEHOUND program, applying carbon and phosphate probes to detect regions with favorable interactions with the probes; generates Jmol-based 3D visualizations and downloadable data files.