pKPDB

pKPDB provides precomputed theoretical pKa and isoelectric point (pI) values for ionizable residues in proteins derived from Protein Data Bank (PDB) structures to support analysis of protein electrostatics, structure, stability, and function.

Key Features:

• Precomputed values: The database contains theoretical pKa and pI values calculated in advance for ionizable residues in proteins.
• Coverage: Over 12 million theoretical pKa values are derived from more than 120,000 protein structures in the Protein Data Bank (PDB).
• Computational methods: pKa estimation uses Poisson-Boltzmann and Monte Carlo calculations.
• Residue-level detail: Values are provided at the level of individual ionizable residues, including buried residues that are often under-represented in experimental measurements.
• Electrostatic focus: Data support analysis of residue electrostatics relevant to protein structure and stability.

Scientific Applications:

• Protein engineering: Use residue pKa and pI values to guide mutagenesis and design decisions affecting stability and activity.
• Drug design: Inform electrostatic complementarity and protonation-state considerations in ligand binding and optimization.
• Protein–ligand interaction studies: Assess how residue protonation states and pI influence binding interfaces and interaction networks.
• Complementing experimental data: Provide theoretical pKa/pI values to augment sparse experimental measurements and to characterize buried residues.

Methodology:

pKa values were estimated from PDB structures using Poisson-Boltzmann and Monte Carlo calculations, and these calculations can require several minutes to hours per calculation.