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MCCE Database (calculated by MCCE1)

Search of residue in protein whose contains

Other Constraints:

pKa/Em range to pH/mV
XRD Resolution smaller than: Angstroms
Protein size: to residues
Residue Burial: to Solvent Accessibility
Desolvation Energy: to delta pK (1 dpK unit =1.36 kcal/mol)

The database is under expanding (currently ~36000 residue pKa values of ~500 structures). Click PDB list for PDB IDs and family names of proteins we have uploaded into the database. The pKas in this database are obtained by MCCE1 program which was used by the paper "Combining Conformational Flexibility and Continuum Electrostatics for Calculating pKas in Proteins". MCCE program has been upgraded to MCCE2 with more extensive rotamer searching, which is now distributed here.

If you use this database please reference:
Are Acidic and Basic Groups in Buried Proteins Predicted to be Ionized? Jinrang Kim, Junjun Mao and M.R. Gunner J.Mol.Biol. April 2005.

How good are these numbersI
We will be expanding this database to include more experimental pKas and pKas calculated by other methods. If you would like to contribute please contact us.

NSFsupport is gratefully acknowledged