PROCHECK

CHECK R Laskowski, M W MacArthur, D S Moss and J M Thornton 1993. Procheck - A program to check the stereochemical quality of protein structures. Journal of Applied Crystallography 26 283-291. 

First, the structure should explain the data. Apart from the energy or target function value returned by the refinement program, this check can be performed with some independent programs (e.g., AQUA/PROCHECK-NMR [90], MOLMOL [91]). The analysis of the deviations from the restraints used in calculating the structures is very useful in the process of assigning the NOE peaks and refining the restraint list. As indicators of the quality of the final structure they are less powerful, because violations have been checked and probably removed. A recent statistical survey of the quality of NMR structures found weak correlations between deviations from NMR restraints and other indicators of structure quality [88]. 

Second, the structures should satisfy the a priori information used in the refinement in the form of the energy parameters. Programs like PROCHECK-NMR check for deviation from expected geometries and close non-bonded contacts. 

Einally, structural properties that depend directly neither on the data nor on the energy parameters can be checked by comparing the structures to statistics derived from a database of solved protein structures. PROCHECK-NMR and WHAT IE [94] use, e.g., statistics on backbone and side chain dihedral angles and on hydrogen bonds. PROSA [95] uses potentials of mean force derived from distributions of amino acid-amino acid distances. 

PROCHECK http //www.biochem.ucl.ac.uk/ roman/procheck/procheck.html... 

An important measure for quality is the verification by MD or SA of the stability of a molecular model. Other programs (e.g., PROCHECK) can also be used to check the globular geometrical quality of a structure to avoid serious defects in the geometry of proteins. 

Validation Once a structure has been determined, it is validated using a custom structure validation system (Badger and Hendle, 2002) to detect local errors. The system is based on PROCHECK (Morris efaJ., 1992), WHATCHECK(Vriend, 1990), SFCHECK (Vaguine ef ah, 1999), and PHISTATS and OVFRLAPMAP (from CCP4). 

The resultant model is subjected to validation, in purely structural and biological aspects. For stereochemical quality, PROCHECK (73), PROVE (74), and Whatlf (75) are among the widely used programs. Programs such as Errat... 

Code used for secondary structure assignments determined by PROCHECK v.3.5. (Laskowski el al., 1993) using the extended Kabsch/Sander classification (Kabsch and Sander, 1983) ... 

Moss, D. S.,Thornton, J. M., PROCHECK A program to check the stereochemical quality of protein stmc-tures,/. Appl. Crystallogr. 1993, 26, 283-291. 

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