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Supported Applications

Reduce

  • Description

    a program for adding hydrogens to a Protein DataBank (PDB) molecular structure file. Hydrogens are added in standardized geometry with optimization of the orientations of OH, SH, NH3+, Met methyls, Asn and Gln sidechain amides, and His rings. Both proteins and nucleic acids can be processed. HET groups can also be processed as long as the atom connectivity is provided.

  • Usage

    To list all executables provided by Reduce, run: $ sbgrid-list reduce Copy to clipboard

  • Usage Notes

    A slightly modified version of the connectivity table published by the PDB is available below. Note that the HET dictionary is available in two "flavors" - new and old (again). Which one to use is dependent upon which type of reduced PDB you want as output.

  • Installation

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

  • Primary Citation*

    J. Word, S. C. Lovell, J. S. Richardson, and D. C. Richardson. 1999. Asparagine and glutamine: using hydrogen atom contacts in the choice of sidechain amide orientation. J Mol Biol. 285(4): 1735-1747.


    • *Full citation information available through

  • Keywords

    Crystallography, NMR

  • Default Versions

    Linux 64:  4.14 (772.0 KB)
    OS X INTEL:  4.14 (777.4 KB)

  • Other Versions

      Linux 64:

      3.14.080821 (674.3 KB) , 3.24.130705 (717.7 KB)

    • OS X INTEL:

      3.14.080821 (614.3 KB) , 3.23.130521 (1.3 MB) , 3.24.130705 (783.1 KB)
    • Common files size: 78.0 MB

  • Developers

    David Richardson, Jane Richardson

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