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Reduce

Reduce is 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. A slightly modified version of the connectivity table published by the PDB is available below. The program is described in Word, et al.(1999) "Asparagine and glutamine: using hydrogen atom contacts in the choice of sidechain amide orientation" J. Mol. Biol. 285, 1735-1747. (download arrow PDF, 804KB)


Item / Platform Version Release date Download size Program
(click to download)
Linux 3.23 21-May-13 747 (Kb) download arrow reduce.3.23.130521.linuxi386.gz
Mac OSX(1)
10.6-10.8
32&64 bit
3.23 21-May-13 488 (Kb) download arrow reduce.3.23.130521.macosx.zip
Windows
Archive cygwin
3.23 21-May-13 1012 (Kb) download arrow reduce.3.23.130521.winArchive.zip
Windows
Installer cygwin
3.23 21-May-13 269 (Kb) download arrow reduce.3.23.130521.winInstall.exe.zip
Source code 3.16 18-Nov-11 19865 (Kb) download arrow reduce.3.16.111118.src.zip
HET dict. 01-Aug-12 01-Aug-12 4.4 (MB) download arrow reduce_wwPDB_het_dict.txt.zip

If you encounter an error in downloading or you are looking for older versions, try to get the file from our browsable download section.
(1)On Mac OS, Reduce is a unix program run from the command-line.
(2)The Windows '*.zip' downloads contain the 1-Aug-2012 version of the HET dict. and a README explaining how to run Reduce on Windows.