pdbFun

pdbFun annotates residues in the Protein Data Bank (PDB) with structural and functional features to enable targeted residue selection and comparative structural analyses.

Key Features:

• Residue-level annotations: Each residue in the PDB is annotated with solvent exposure, ligand binding capability, spatial location within protein cavities, secondary structure classification, residue type, sequence functional patterns, domain associations, and catalytic activity.
• Mass selection by annotation: Users can create residue subsets across any number of PDB structures by combining multiple annotation features.
• Comparative searches: Fast comparison searches enable matching selected residue subsets against single protein structures or large structural datasets.
• Complex query criteria: Queries can specify criteria such as solvent exposure, hydrophilicity, absence from secondary structures (e.g., not in alpha-helices), and involvement in functions like nucleotide binding.
• Aligned results presentation: Search results present aligned structural matches in tabular and graphical formats for interpretation and analysis.

Scientific Applications:

• Functional residue identification: Identify catalytic or binding residues by selecting residues based on functional annotations such as ligand binding or catalytic activity.
• Evolutionary and functional comparison: Compare selected residue subsets across structural datasets to identify conserved features and support evolutionary or functional studies.
• Structural motif distribution analysis: Investigate distributions of motifs (for example, solvent-exposed hydrophilic residues) within protein families or complexes.

Methodology:

pdbFun organizes PDB data at the residue level and integrates diverse annotation features into a database to enable precise querying and comparison of residue subsets.