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SITEHOUND-web: a server for ligand binding site identification in protein structures
Marylens Hernandez1, Dario Ghersi, Roberto Sanchez
1Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, NY 10029, USA.
Nucleic Acids Research
|April 29, 2009
Summary
SITEHOUND-web identifies potential ligand binding sites on protein structures using specific molecular probes. This web server aids in drug discovery and understanding molecular interactions by visualizing and providing data on these predicted sites.
Area of Science:
- Structural Biology
- Computational Chemistry
- Bioinformatics
Background:
- Identifying ligand binding sites on proteins is crucial for understanding biological functions and for drug discovery.
- Existing methods may have limitations in accuracy, speed, or scope of detectable binding sites.
Purpose of the Study:
- To introduce SITEHOUND-web, a web server for identifying putative ligand binding sites on protein structures.
- To provide a user-friendly platform for exploring potential binding pockets using different molecular probes.
Main Methods:
- SITEHOUND-web utilizes the SITEHOUND program, which analyzes protein structures (PDB format).
- It employs molecular probes (e.g., carbon for drug-like molecules, phosphate for phosphorylated ligands) to detect favorable interaction regions.
- Results are presented via interactive HTML pages with Jmol 3D visualizations and downloadable data files.
Main Results:
- The server successfully identifies potential binding sites based on probe interactions.
- It offers distinct analyses for different ligand types (drug-like molecules, phosphorylated ligands).
- Interactive 3D models and downloadable data facilitate further analysis.
Conclusions:
- SITEHOUND-web provides a valuable, accessible tool for predicting ligand binding sites.
- The server supports research in structural biology, drug design, and molecular interactions.
- Its interactive features and data output enhance the utility for researchers.
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