1. Introduction

Hui Li, Andrew D. Robertson and Jan H. Jensen developed a very fast empirical method for protein pK_a prediction and rationalization (PROTEINS: Structure, Function and Bioinformatics 61:704-21, 2005). The desolvation effects and intra-protein interactions, which cause variations in pK_a values of protein ionizable groups, are empirically related to the positions and chemical nature of the groups proximate to the pK_a sites. The Authors developed a program (PROPKA) to automatically predict pK_a values based on these empirical relationships within a couple of seconds. Unusual pK_a values at buried active sites, which are among the most interesting protein pK_a values, are predicted very well with the empirical method.
With the kind permission of the Authors, the PROPKA executable is included in the VEGA ZZ package and now is accessible trough the VEGA On-line service.

2. How it works

The user send the molecule to the server that automatically converts it to PDB 2.2 thanks to VEGA. The output is passed to PROPKA and its output is converted to the HTML format and sent to the user.

3. Papers

• Hui Li, Andrew D. Robertson, and Jan H. Jensen "Very Fast Empirical Prediction and Interpretation of Protein pK_a Values"Proteins, 2005, 61, 704-721.
• N. Powers and Jan H. Jensen "Chemically Accurate Protein Structures:Validation of Protein NMR Structures by Comparison of Measured and Predicted pK_a Values", J. Biomolecular NMR 2006, 35, 39-51.
• Melissa A. Porter, Jordan R. Hall, James C. Locke, Jan H. Jensen and Pablo A. Molina "Amide Backbone Interactions are the Prime Determinants of Carboxyl pK_a Values at N-termini of alpha-helices" Proteins: Structure, Function, and Bioinformatics, 63, 621 - 635.
• MN Davies, CP Toseland, DS Moss and DR Flower "Benchmarking pK_a Predictions" BMC Biochemistry 2006, 7, 18.

5. Copyright

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free SoftwareFoundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.

PROPKA
is a software developed in 2004-2013
by Jan H. Jensen, Andrew D. Robertson, Hui Li, David M. Rogers
All rights reserved.

Jan H. Jensen
Department of Chemistry
University of Copenaghen
Universitetsparken 5
2100 Copenhagen - Denmark
Tel. +45 35 32 02 39
Fax. +45 35 32 02 14
E-Mail: jhjensen@kemi.ku.dk
WWW: http://propka.ki.ku.dk/~jhjensen/