Reduce

Reduce (DOI:10.1006/jmbi.1998.2401) is a protonation software made for use with Probe. Packaged with RINRUS because that’s what we use for protonating initial PDB structures.

Reduce can flip orientation of certain residues when protonating. We avoid this with NOFLIP option.

Reduce uses the PDB HET ligand dictionary (provided with RINRUS as reduce_wwPDB_het_dict.txt) to protonate non-canonical residues, small molecules, ligands etc. See installation instructions for making sure this is accessible to Reduce.

Example usage of reduce with our standard options

$HOME/git/RINRUS/bin/reduce -NOFLIP 3bwm.pdb > 3bwm_h.pdb

Inputs:

• Unprotonated PDB file

Outputs:

• Protonated PDB file