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Supported Applications

PDB2PQR

  • Description

    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

  • Primary Citation*

    T. Dolinsky, P. Czodrowski, H. Li, J. Nielsen, J. Jensen, G. Klebe, and N. Baker. 2007. PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res. 35: 522-525.
    (Note: Web Server Issue, W522-W525)


    • *Full citation information available through

  • Categories

    Computational Chemistry

  • Default Versions

    Linux 64:  2.1
    OS X INTEL:  2.1

  • Other Available Versions

      Linux 32:

      1.8
    • Linux 64:

      1.8
    • OS X INTEL:

      1.8
  • Developers

    Nathan Baker.

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