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Table 2 Predicted vs. experimental pKa shifts

From: Bluues: a program for the analysis of the electrostatic properties of proteins based on generalized Born radii

 

BLUUES

Propka v. 2.0

 

RMSD

corr. coef.

RMSD

corr. coef.

ASP

0.78

0.42

1.50

0.27

GLU

0.90

0.54

1.75

0.24

HIS

0.98

0.74

1.50

0.59

LYS

0.79

0.45

0.79

0.25

TYR

1.78

0.41

2.12

-0.03

NTR

0.54

0.93

0.96

-1.00

CTR

1.01

-0.14

1.06

0.36

All

1.00

0.51

1.59

0.36

  1. Comparison of predicted vs. experimental pKa's. The RMSD is reported together with the correlation coefficient. We report the results obtained using Propka v.2.0. The latter program is very accurate, but occasional large shifts, not filtered nor treated ad-hoc here, result in large RMSD and smaller correlation coefficients.
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BMC Bioinformatics

ISSN: 1471-2105

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