3D Structure Prediction Bioinformatics Bioinformatics Tool Structure Evaluation

ProCheck

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The PROCHECK is a suite of programs that provides a detailed check on the stereochemistry of a protein structure. Its outputs are consisted of a number of plots in PostScript format and a comprehensive residue-by-residue listing. These give an assessment of the overall quality of the structure as compared with well refined structures of the same resolution and also highlight regions that may need further investigation. The PROCHECK programs are useful for assessing the quality not only of protein structures in the process of being solved but also of existing structures and of those being modeled on known structures. It uses PROCHECK-NMR for checking the quality of structures solved by NMR.

PROCHECK-NMR is a suite of programs that produce PostScript plots of the restraint violations computed by AQUA together with certain analyses of the stereo chemical quality of the models in the NMR ensemble.

The inputs are consisted of;

The PDB file having the coordinates of the structure of interest, this must be in Brookhaven file format, with each model in the ensemble separated by the correct MODEL and ENDMDL records, an (optional) restraint file listing the NOEs, Hydrogen-bonds, disulphides, generic distance and torsion angle restraints used in solving the structure, an (optional) model- and residue-blocks file listing the model- and residue-ranges to which the analyses are to be restricted. One of the by-products of running  PROCHECK is that our coordinates file will be “cleaned up” by the first of the programs. The cleaning-up process corrects any mislabeled atoms and creates a new coordinates file which has a file-extension of .new. The .new file will have the atoms labeled in accordance with the IUPAC naming conventions.

The outputs from the programs are:

The outputs are consisted of a number of plots, together with a detailed residue-by-residue listing. Certain formatted text files show the AQUA analyses. These can be further summarized and sub-analyzed using the various tools provided by AQUA.

PostScript files show the PROCHECK-NMR analyses. The appearance of the plots can be modified to some extent according to our need.

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 (e.g. distortions due to ligand-binding in the protein’s active site). The stereochemical parameters are used in PROCHECK. These parameters are mostly used in standard refinement procedures.

The checks also make use of “ideal” bond lengths and bond angles, as derived from a recent and comprehensive analysis of small molecule structures in the Cambridge Structural Database, CSD.

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