[Debichem-devel] Bug#438092: ITP: pdb2pqr -- An automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations

[LI Daobing]

Package: wnpp
Severity: wishlist
Owner: LI Daobing <lidaobing at gmail.com>

* Package name    : pdb2pqr
  Version         : 1.2.1
  Upstream Author : jens_nielsen, sobolevnrm, todd_dolinsky
* URL             : exec /usr/lib/autossh/autossh
* License         : GPL
  Programming Lang: Python
  Description     : 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.