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PROCHECK: validation of protein-structure coordinates
Laskowski, R. A., MacArthur, M. W. and Thornton, J. M.  International Tables for Crystallography (2012). Vol. F, ch. 21.4, pp. 684-687 [ doi:10.1107/97809553602060000882 ]
... As in all scientific measurements, the parameters that result from a macromolecular structure determination by X-ray crystallography (e.g. atomic coordinates ... model, as well as the reliability of the model as a whole. Among these methods are those that rely on checking ... without reference to the experimental data (MacArthur et al., 1994; Laskowski et al., 1998). Here we describe PROCHECK (Laskowski ...

Output produced
Laskowski, R. A., MacArthur, M. W. and Thornton, J. M.  International Tables for Crystallography (2012). Vol. F, Section 21.4.6, p. 686 [ doi:10.1107/97809553602060000882 ]
... 21.4.6. Output produced The output of the program consists of a number of PostScript plots, together with a full listing of the individual parameter values for each residue ... highlighted. The listing also provides summaries for the protein as a whole. Figs. 21.4.6.1 and 21.4.6.2 show parts of one ...

Input
Laskowski, R. A., MacArthur, M. W. and Thornton, J. M.  International Tables for Crystallography (2012). Vol. F, Section 21.4.5, p. 686 [ doi:10.1107/97809553602060000882 ]
Input 21.4.5. Input The primary input to PROCHECK is the file containing the 3D coordinates of the protein structure to be processed. The file is required to be in PDB format. An additional input file is the parameter file that governs which plots are to be generated and deals with certain ...

Which parameters are best?
Laskowski, R. A., MacArthur, M. W. and Thornton, J. M.  International Tables for Crystallography (2012). Vol. F, Section 21.4.4, p. 685 [ doi:10.1107/97809553602060000882 ]
... the most telling and useful of the `quality' indicators for a protein model is the Ramachandran plot of residue [varphi]-[psi ... how densely they are populated with data points taken from a database of well refined protein structures. The regions are: core ... . Fig. 21.4.4.1 shows the original PROCHECK Ramachandran plot and a more up-to-date version. The original was based ...

The parameters
Laskowski, R. A., MacArthur, M. W. and Thornton, J. M.  International Tables for Crystallography (2012). Vol. F, Section 21.4.3, pp. 684-685 [ doi:10.1107/97809553602060000882 ]
... protein quality. The table shows the original parameters together with a more up-to-date set derived from a more recent data set including a number of atomic resolution structures (i.e. those solved to ...

The program
Laskowski, R. A., MacArthur, M. W. and Thornton, J. M.  International Tables for Crystallography (2012). Vol. F, Section 21.4.2, p. 684 [ doi:10.1107/97809553602060000882 ]
The program 21.4.2. The program PROCHECK is in fact a suite of separate Fortran and C programs which are run successively via a shell script. The programs first `clean up' the input PDB ... against the norms, and finally generate the PostScript output and a detailed residue-by-residue listing. Hydrogen and atoms with ...

Introduction
Laskowski, R. A., MacArthur, M. W. and Thornton, J. M.  International Tables for Crystallography (2012). Vol. F, Section 21.4.1, p. 684 [ doi:10.1107/97809553602060000882 ]
... As in all scientific measurements, the parameters that result from a macromolecular structure determination by X-ray crystallography (e.g. atomic coordinates ... model, as well as the reliability of the model as a whole. Among these methods are those that rely on checking ... without reference to the experimental data (MacArthur et al., 1994; Laskowski et al., 1998). Here we describe PROCHECK (Laskowski ...

Other validation tools
Laskowski, R. A., MacArthur, M. W. and Thornton, J. M.  International Tables for Crystallography (2012). Vol. F, Section 21.4.7, p. 686 [ doi:10.1107/97809553602060000882 ]
... tools 21.4.7. Other validation tools PROCHECK is merely one of a number of validation tools that are freely available, some of ... QUANTA (MSI, 1997) provide standard tests on the geometry of a structure and provide lists of residues with unexpected features, which ... San Diego, CA 92121-3752, USA. Eisenberg, D., Lüthy, R. & Bowie, J. U. (1997). VERIFY3D: assessment of protein ...

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