# PDB2PQR

### An automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations.

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:

- Adding a limited number of missing heavy atoms to biomolecular structures
- Determining side-chain pKas
- Placing missing hydrogens
- Optimizing the protein for favorable hydrogen bonding
- Assigning charge and radius parameters from a variety of force fields

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:

- Documentation:
  - User Guide
  - Programmer Guide
  - Examples
- Availability
- Mailing lists
- Further Reading/Citing PDB2PQR
- Supporting organizations
- License
- PDB2PQR Usage Statistics (WUSTL Mirror)

### Availability

PDB2PQR is available as both a web service and as command-line software for download. The PDB2PQR web server can be found at two mirrors:

- Washington University in St. Louis (currently running version 1.8)
- NBCR (UCSD) (currently running version 1.8)

The command line PDB2PQR tool is freely available for download.

### Mailing Lists

There are two mailing lists associated with the PDB2PQR software:

- pdb2pqr-announce, a low-traffic list for announcements regarding bugs and new versions of the software: List web page, List archives
- pdb2pqr-users, a list for discussion of PDB2PQR, troubleshooting, and reporting potential bugs: List web page, List archives

### Further Reading/Citing PDB2PQR

Please acknowledge your use of PDB2PQR by citing:

- Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA. PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res, 35, W522-5, 2007.
- 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 Res, 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).

### Supporting Organizations

The development of PDB2PQR has been supported financially by:

- National Institutes of Health (grant GM069702-01)
- National Partnership for Advanced Computational Infrastructure Alpha Project program
- National Biomedical Computation Resource

SourceForge Project Page

Last changed on: $Date: 2007-02-10 11:06:05 -0600 (Sat, 10 Feb 2007)$