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<head>
<title>PDB2PQR</title>
<link rel="stylesheet" href="http://agave.wustl.edu/css/baker.css"
type="text/css">
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<body>
<center>
<h1>PDB2PQR</h1>
<h3>An automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations.</h3>
</center>
<HR>
<p> 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 <a href="http://www.rcsb.org/pdb/">PDB format</a> to
PQR format. These tasks include:
<ul>
<li> Adding a limited number of missing heavy atoms to
biomolecular structures
<li> Determining side-chain pKas
<li> Placing missing hydrogens
<li> Optimizing the protein for favorable hydrogen bonding
<li> Assigning charge and radius parameters from a variety of
force fields
</ul>
<p> PDB2PQR was ported to Python by Todd Dolinsky while working with <a
href="http://agave.wustl.edu">Nathan Baker</a> at Washington
University in St. Louis. The PDB2PQR code is based on C++ design and
algorithms by <a href="http://enzyme.ucd.ie/">Jens Erik Nielsen</a>.
PDB2PQR was originally designed to facilitate structure preparation for
<a href="http://apbs.wustl.edu">APBS</a>.
<p> PDB2PQR uses <a href="http://propka.ki.ku.dk">PROPKA</a> to
determine protein pKa values. PROPKA is developed by the <a
href="http://propka.ki.ku.dk/~jhjensen/">Jensen Research
Group</a> at the University of Copenhagen. More information
about PROPKA can be found at <a
href="http://propka.ki.ku.dk/">http://propka.ki.ku.dk/</a>.<P>
<p> PEOE_PB charges for
<!--biomolecue and -->
ligand parameterization were
developed by Paul Czodrowski in the <a
href="http://www.agklebe.de">Klebe Group</a> at the Philipps University Marburg.
<p> Please visit the following links for more information about PDB2PQR:
<ul>
<li>Documentation:
<ul>
<li> <a href="userguide.html">User
Guide</a> </li>
<li> <a href="programmerguide.html">Programmer
Guide</a> </li>
<li> <a href="examples/">Examples</a> </li>
</ul>
<li><a href="#availability">Availability</a>
<li><a href="#mailing">Mailing lists</a>
<li><a href="#citing">Further Reading/Citing PDB2PQR</a>
<li><a href="#support">Supporting organizations</a>
<li><a href="license.txt">License</a>
<li> <a href="http://agave.wustl.edu/pdb2pqr-stats/usage/">PDB2PQR
Usage Statistics</a> (WUSTL Mirror) </li>
</ul>
<hr>
<a name="availability"></a>
<h3>Availability</h3>
<P> 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:
<ul>
<li> <a href="http://agave.wustl.edu/pdb2pqr/index.html">Washington
University in St. Louis</a> (currently running
version 1.8)
<li><a href="http://nbcr.net/pdb2pqr">NBCR (UCSD)</a>
(currently running
version 1.8)
</ul>
<P> The command line PDB2PQR tool is freely available for <a
href="http://agave.wustl.edu/pdb2pqr-stats/register.html">download</a>.
<hr/>
<a name="mailing"></a>
<h3>Mailing Lists</h3>
<P> There are two mailing lists associated with the PDB2PQR
software:
<ul>
<li>pdb2pqr-announce, a low-traffic list for announcements
regarding bugs and new versions of the software: <a
href="http://lists.sourceforge.net/lists/listinfo/pdb2pqr-announce">List
web page</a>, <a
href="http://sourceforge.net/mailarchive/forum.php?forum=pdb2pqr-announce">List
archives</a>
<li>pdb2pqr-users, a list for discussion of PDB2PQR,
troubleshooting, and reporting potential bugs: <a
href="http://lists.sourceforge.net/lists/listinfo/pdb2pqr-users">List
web page</a>, <a
href="http://sourceforge.net/mailarchive/forum.php?forum=pdb2pqr-users">List
archives</a>
</ul>
<HR/>
<a name="citing"></a> <h3>Further Reading/Citing PDB2PQR</h3><P>
<p>Please acknowledge your use of PDB2PQR by citing:
<ul>
<li> <a href="http://dx.doi.org/10.1093/nar/gkm276">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. <i>Nucleic Acids Res</i>, <b>35</b>, W522-5, 2007.</a> </li>
<li> <a href="http://nar.oupjournals.org/cgi/content/abstract/32/suppl_2/W665">Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. <i>Nucleic Acids Res</i>, <b>32</b>, W665-W667 (2004).</a> </li>
</ul>
</p>
<p>Please acknowledge your use of PropKa by citing:
<blockquote>
<a href="http://dx.doi.org/10.1002/prot.20660">Li H, Robertson
AD, Jensen JH. Very Fast Empirical Prediction and
Rationalization of Protein pKa Values. <i>Proteins</i>,
<b>61</b>, 704-721 (2005).</a>
</blockquote>
<p>Please acknowledge your use of PEOE_PB charges by citing:
<blockquote>
<a href="http://dx.doi.org/10.1002/prot.21110">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. <i>Proteins</i>, <b>65</b>,
424-437 (2006).</a>
</blockquote>
<HR/>
<a name="support"></a>
<h3>Supporting Organizations</h3>
<P> The development of PDB2PQR has been supported financially by:
<ul>
<li><a href="http://www.nih.gov/">National Institutes of
Health</a> (grant GM069702-01)
<li><a href="http://www.npaci.edu/">National Partnership for
Advanced Computational Infrastructure</a> Alpha Project
program
<li><a href="http://nbcr.sdsc.edu/">National Biomedical
Computation Resource</a>
</ul>
<hr/>
<center>
<a href="http://sourceforge.net/projects/pdb2pqr">SourceForge Project Page</a>
</center>
<hr/>
<center>
<small>
Last changed on: $Date: 2007-02-10 11:06:05 -0600 (Sat, 10 Feb 2007)$
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