PROCHECK Operating Manual

1. Introduction

Aims

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 checked carefully.

Stereochemical parameters

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.

Input

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 Nomenclature, 1970).

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.

Outputs

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.

Programs

The suite comprises a number of programs which are described in Appendix C.