Section 21.3.3.1.  PROCHECK

The PROCHECK (Laskowski et al., 1993) suite of programs compares the stereochemistry of a proposed protein model to stereochemical features of known structures. The program provides an assessment of the overall quality of the model by comparing the model with well refined structures of the same resolution, and also highlights regions that may need further adjustment. The output of PROCHECK comprises a number of plots, together with detailed residue-by-residue listings of secondary-structure assignment, non-bonded interactions between different pairs of residues, main-chain bond lengths and bond angles, and peptide-bond planarity.

The program also displays main-chain dihedral angles (φ and ψ) as a two-dimensional Ramachandran (Ramachandran & Sasisekharan, 1968) plot. The Ramachandran plot classifies each residue in one of three categories: `allowed' conformations; `partially allowed' conformations, which give rise to modestly unfavourable repulsion between non-bonded atoms, and which might be overcome by attractive effects such as hydrogen bonds; and `disallowed' interactions which give highly unfavourable non-bonded interatomic distances. The Ramachandran plot can identify unacceptable clusters of – angles, revealing possible errors made during model building and refinement. As opposed to covalent bond angles and bond lengths, the main-chain dihedral angles are not usually restrained during X-ray refinement and therefore can be used to validate the structural model independently. In practice, the Ramachandran plot is one of the simplest, most sensitive tools for assessing the quality of a protein model.

The PROCHECK suite is generally useful for assessing the quality of protein structures in various stages of completion. The Ramachandran analysis is especially informative. However, it is possible, at least in principle, to devise an incorrect model with fully acceptable main-chain and side-chain stereochemistry, so other methods must also be used to assess protein models.