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propka3.1 2013-11-28
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-- --
-- PROPKA: A PROTEIN PKA PREDICTOR --
-- --
-- VERSION 1.0, 04/25/2004, IOWA CITY --
-- BY HUI LI --
-- --
-- VERSION 2.0, 11/05/2007, IOWA CITY/COPENHAGEN --
-- BY DELPHINE C. BAS AND DAVID M. ROGERS --
-- --
-- VERSION 3.0, 01/06/2011, COPENHAGEN --
-- BY MATS H.M. OLSSON AND CHRESTEN R. SONDERGARD --
-- --
-- VERSION 3.1, 07/01/2011, COPENHAGEN --
-- BY CHRESTEN R. SONDERGARD AND MATS H.M. OLSSON --
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References:
Very Fast Empirical Prediction and Rationalization of Protein pKa Values
Hui Li, Andrew D. Robertson and Jan H. Jensen
PROTEINS: Structure, Function, and Bioinformatics 61:704-721 (2005)
Very Fast Prediction and Rationalization of pKa Values for Protein-Ligand Complexes
Delphine C. Bas, David M. Rogers and Jan H. Jensen
PROTEINS: Structure, Function, and Bioinformatics 73:765-783 (2008)
PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa predictions
Mats H.M. Olsson, Chresten R. Sondergard, Michal Rostkowski, and Jan H. Jensen
Journal of Chemical Theory and Computation, 7(2):525-537 (2011)
Improved Treatment of Ligands and Coupling Effects in Empirical Calculation
and Rationalization of pKa Values
Chresten R. Sondergaard, Mats H.M. Olsson, Michal Rostkowski, and Jan H. Jensen
Journal of Chemical Theory and Computation, (2011)
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DESOLVATION EFFECTS SIDECHAIN BACKBONE COULOMBIC
RESIDUE pKa BURIED REGULAR RE HYDROGEN BOND HYDROGEN BOND INTERACTION
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SUMMARY OF THIS PREDICTION
Group pKa model-pKa ligand atom-type
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Free energy of folding (kcal/mol) as a function of pH (using neutral reference)
0.00 0.00
1.00 0.00
2.00 0.00
3.00 0.00
4.00 0.00
5.00 0.00
6.00 0.00
7.00 0.00
8.00 0.00
9.00 0.00
10.00 0.00
11.00 0.00
12.00 0.00
13.00 0.00
14.00 0.00
The pH of optimum stability is 0.0 for which the free energy is 0.0 kcal/mol at 298K
Could not determine pH values where the free energy is within 80 % of minimum
Could not determine the pH-range where the free energy is negative
Protein charge of folded and unfolded state as a function of pH
pH unfolded folded
0.00 0.00 0.00
1.00 0.00 0.00
2.00 0.00 0.00
3.00 0.00 0.00
4.00 0.00 0.00
5.00 0.00 0.00
6.00 0.00 0.00
7.00 0.00 0.00
8.00 0.00 0.00
9.00 0.00 0.00
10.00 0.00 0.00
11.00 0.00 0.00
12.00 0.00 0.00
13.00 0.00 0.00
14.00 0.00 0.00
The pI is 0.00 (folded) and 0.00 (unfolded)
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