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PDB2PQR

  • Description

    a Python package that automates structure preparation tasks for continuum electrostatics calculations. It can convert protein files in PDB format to PQR format. It can add a limited number of missing heavy atoms to biomolecular structures, determine side-chain pKas, placing missing hydrogens, optimize the protein for favorable hydrogen bonding, and assign charge and radius parameters from a variety of force fields.

  • Usage

    To list all executables provided by PDB2PQR, run: $ sbgrid-list pdb2pqr Copy to clipboard

  • Installation

    Use the following command to install this title with the CLI client: $ sbgrid-cli install pdb2pqr Copy to clipboard Available operating systems: Linux 64, OS X INTEL

  • 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

  • Keywords

    Computational Chemistry

  • Default Versions

    Linux 64:  2.1 (48.8 MB)
    OS X INTEL:  2.1 (27.1 MB)

  • Other Versions

      Linux 64:

      1.8 (7.8 MB)

    • OS X INTEL:

      1.8 (23.6 MB)

  • Developers

    Nathan Baker

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