PROCHECK program

PROCHECK Program to evaluate the stereochemical quality of protein structures 179 www.biochem.ucl.ac.uk/ roman/procheck/ procheck.html... 

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. 

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. 

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... 

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

Side chain atom packing of amino acid residues has been an important structural quality measure in X-ray.112,113 The structural quality criteria are also introduced for NMR structure quality checks.50,114 However, almost, all NMR structures deposited in PDB uniformly have poor scores for the side chain packing. There is no consensus whether X-ray packing-derived structural criteria can be used for NMR quality check. Some checking programs are available in PDB, e.g., PROCHECK,115 PROCHECK-NMR,116 and WHAT-CHECK.117... 

Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK a program to... 

In the sections that follow, the algorithms of PROCHECK, WHATCHECK, VerifySD, ERRAT, and PROVE will be described individually, and program outputs illustrated and interpreted for the particular case, PDB ID code lja3 (Dimasi et al., 2002). After surveying all the stmctures deposited in the PDB, lja3 was flagged... 

The PROCHECK stmcture validation program (Laskowski et al, 1993) deploys a multitude of quality checks using both aoss-validation and standard checks for geometric deviations. The Ramachandran plot it produces is its most attractive and useful feature (Ramakrishnan and Ramachandran, 1965). The plot consists of a two dimensional plot of phi/psi values for each amino acid residue. Steric overlap between side chain and main chain atoms limits the energetically allowed values... 

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