PROCHECK Operating Manual
These Operating Instructions describe how to run the PROCHECK suite
of programs (Laskowski et al., 1993) for
assessing the "stereochemical quality" of a given protein
structure. The instructions assume that the programs have already been
installed on your computer system. If this is not the case, please refer to
the separate Installation Guide which deals with the installation
procedures for your particular system.
The aim of PROCHECK is to assess how normal, or conversely
how unusual, the geometry of the residues in a given protein
structure is, as compared with stereochemical parameters derived from
well-refined, high-resolution structures.
Unusual regions highlighted by PROCHECK are not necessarily
errors as such, but may be unusual features for which there
is a reasonable explanation (eg distortions due to ligand-binding
in the protein's active site). Nevertheless they are regions that should be
The stereochemical parameters used are those described in detail in Morris et al. (1992). These parameters, which
are for the most part not included in standard refinement procedures (and
so are less likely to be biased by them), are listed in Table 1 of Appendix A.
The checks also make use of "ideal" bond lengths and bond angles,
as derived from a recent and comprehensive analysis (Engh & Huber, 1991) of small molecule
structures in the Cambridge Structural Database, CSD (Allen et al., 1979) - now numbering over
100,000 structures. These "ideal" values are listed in Table 2 of Appendix A.
The input to PROCHECK is a single file containing the coordinates of
your protein structure. This must be in Brookhaven file format (see Appendix B). One of the by-products of running
PROCHECK is that your coordinates file will be "cleaned
up" by the first of the programs. The cleaning-up process corrects any
mislabelled atoms and creates a new coordinates file which has a
file-extension of .new. The .new file will have the atoms
labelled in accordance with the IUPAC naming conventions (IUPAC-IUB Commission of Biochemical
Note. At present, hydrogen atoms are ignored. Atoms with zero
occupancy are omitted from the analyses and only the highest occupancy
conformations are retained wherever there are alternate conformations.
The outputs comprise a number of plots, together with a detailed
residue-by-residue listing. The plots are output in PostScript format (Adobe Systems Inc., 1985), and so can be
printed off on a PostScript laser printer, or displayed on a graphics
screen using suitable software (eg GHOSTSCRIPT or
GHOSTVIEW on Sun or Silicon Graphics workstations, or PSVIEW
on Silicon Graphics IRIS-4D systems). The plots can be in colour or
black-and-white and are described in Sample plots. The residue-by-residue
listing is described in Appendix D.
The suite comprises a number of programs which are described in Appendix C.
PROCHECK Operating Manual