Section 25.2.6.1. Introduction

As in all scientific measurements, the parameters that result from a macromolecular structure determination by X-ray crystallography (e.g. atomic coordinates and B factors) will have associated uncertainties. These arise not only from systematic and random errors in the experimental data but also in the interpretation of those data. Currently, the uncertainties cannot easily be estimated for macromolecular structures due to the computer- and memory-intensive nature of the calculations required (Tickle et al., 1998). Thus, more indirect methods are necessary to assess the reliability of different parts of the model, as well as the reliability of the model as a whole. Among these methods are those which rely on checking only the stereochemical and geometrical properties of the model itself, without reference to the experimental data (MacArthur et al., 1994; Laskowski et al., 1998). Here we describe PROCHECK (Laskowski et al., 1993), which is one of these structure-validation methods.

The PROCHECK program computes a number of stereochemical parameters for the given protein model and compares them with `ideal' values obtained from a database of well refined high-resolution protein structures in the Protein Data Bank (PDB; Bernstein et al., 1977). The results of these checks are output in easy-to-understand coloured plots in PostScript format (Adobe Systems Inc., 1985). Significant deviations from the derived standards of normality are highlighted as being `unusual'.

The program's primary use is during the refinement of a protein structure; the highlighted regions can direct the crystallographer to parts of the structure that may have problems and which may need attention. It should be noted that outliers may just be outliers; they are not necessarily errors. Unusual features may have a reasonable explanation, such as distortions due to ligand binding in the protein's active site. However, if there are many oddities throughout the model, this could signify that there is something wrong with it as a whole. Conversely, if a model has good stereochemistry, this alone is not proof that it is a good model of the protein structure.

Because the program requires only the 3D atomic coordinates of the structure, it can check the overall `quality' of any model structure: whether derived experimentally by crystallography or NMR, or built by homology modelling. In the case of NMR-derived structures, it is useful to compare the protein geometry across the whole ensemble. An extended version of PROCHECK, called PROCHECK-NMR, is available for this purpose (Laskowski et al., 1996), but will not be described here.

Note that PROCHECK only examines the geometrical properties of protein molecules; it ignores DNA/RNA and other non-protein molecules in the structure, except in so far as checking that the non-bonded contacts these make with the protein do not violate a fixed distance criterion.