The PROPKA Web Interface 2.0

Created by Donald Ephraim Curtis with help from Todd Dolinsky and Nathan Baker

PROPKA 2.0 added by David M. Rogers

Use PROPKA and PDB2PQR to add hydrogens to your x-ray structure: PDB2PQR

PROPKA 2.0 includes ligands in pKa prediction and will use the first conformer set. Tutorial.

NEW: PROPKA/Jmol interface on the web server (blue links in output)

NEW: PROPKA plug-in for VMD can be downloaded here

References.

Register and download the PROPKA 2.0 source code and scripts: PROPKA 2.0 Download.


Please enter either:
a PDB ID:
upload a PDB file:
PDB file web address:

Specify PDB chain IDs (separated by a comma ","):

Include ligands: Enabling this will include ligands. Disabling will use PROPKA 1.0.

Or upload a "new_PDB" PROPKA 2.0 input file:

For assistance see the PROPKA 2.0 Tutorial. (Please report errors to "chresten _at_ kemi.ku.dk".)

The PROPKA method is developed by the
Jensen Research Group
Department of Chemistry
University of Copenhagen

Please cite these references in publications:

Hui Li, Andrew D. Robertson, and Jan H. Jensen "Very Fast Empirical Prediction and Interpretation of Protein pKa Values" Proteins, 2005, 61, 704-721.

Delphine C. Bas, David M. Rogers, and Jan H. Jensen "Very Fast Prediction and Rationalization of pKa Values for Protein-Ligand Complexes" Proteins, 2008, 73, 765-783.

Reprints can be obtained by contacting Jan Jensen.

For more information see the PROPKA 2.0 Wiki.

Register and download the PROPKA 2.0 source code and scripts: PROPKA 2.0 Download.



Last Updated June 24th, 2009