PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format. These tasks include:
PDB2PQR was ported to Python by Todd Dolinsky while working with Nathan Baker at Washington University in St. Louis. The PDB2PQR code is based on C++ design and algorithms by Jens Erik Nielsen. PDB2PQR was originally designed to facilitate structure preparation for APBS.
PDB2PQR uses PROPKA to determine protein pKa values. PROPKA is developed by the Jensen Research Group at the University of Copenhagen. More information about PROPKA can be found at http://propka.ki.ku.dk/.
PEOE_PB charges for ligand parameterization were developed by Paul Czodrowski in the Klebe Group at the Philipps University Marburg.
Please visit the following links for more information about PDB2PQR:
PDB2PQR is available as both a web service and as command-line software for download. The PDB2PQR web server can be found at three mirrors:
The command line PDB2PQR tool is freely available for download.
There are two mailing lists associated with the PDB2PQR software:
Please acknowledge your use of PDB2PQR by citing:
Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Research, 32, W665-W667 (2004).
Please acknowledge your use of PropKa by citing:
Li H, Robertson AD, Jensen JH. Very Fast Empirical Prediction and Rationalization of Protein pKa Values. Proteins, 61, 704-721 (2005).
Please acknowledge your use of PEOE_PB charges by citing:
Czodrowski P, Dramburg I, Sotriffer CA, Klebe G. Development, validation, and application of adapted PEOE charges to estimate pKa values of functional groups in protein-ligand complexes. Proteins, 65, 424-437 (2006).
The development of PDB2PQR has been supported financially by: