StarPDB

StarPDB provides structural annotation of protein sequences by performing BLAST-based similarity searches against the Protein Data Bank (PDB) and applying residue-level annotation modules to predict secondary structure, accessible surface area (ASA), tight turns (including beta-turns), DNA/RNA interactions, and ligand/metal/nucleotide binding.

Key Features:

• BLAST-Based Similarity Search: Uses the standard BLAST software to search query proteins against structures in the Protein Data Bank (PDB) to identify structural analogs.
• Secondary Structure Prediction: Predicts regular secondary structure states for each residue, including alpha-helices and beta-sheets.
• Accessible Surface Area (ASA) Analysis: Predicts residue-level exposure to identify buried versus exposed residues.
• Tight-Turns Prediction: Identifies tight turns such as beta-turns to refine local backbone conformation annotation.
• DNA/RNA Interaction Prediction: Predicts residues that interact with DNA or RNA to annotate potential nucleic acid-binding sites.
• Ligand Interaction Prediction: Identifies residues interacting with ligands, metals, and nucleotides to annotate binding sites.
• Visualization Tools: Provides visualization of structural and functional residue annotations to interpret predicted features in the context of protein structure.

Scientific Applications:

• Functional Annotation: Supports hypothesis generation for protein function by predicting interaction sites and secondary structure.
• Protein Engineering: Informs selection of exposed residues and binding-site residues for targeted mutations or design.
• Drug Discovery: Identifies ligand-binding residues and metal/nucleotide interaction sites relevant to target identification and lead optimization.

Methodology:

Integrates BLAST-based similarity searches against the PDB with a suite of specialized residue-level annotation modules for secondary structure, ASA, tight turns, DNA/RNA interactions, and ligand interactions.