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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 ]
... include David K. Smith, E. Gail Hutchinson, David T. Jones, J. Antoon C. Rullmann, A. Louise Morris and Dorica Naylor. Part ... Peters, B. G., Kennard, O., Motherwell, W. D. S., Rodgers, J. R. & Watson, D. G. (1979). The Cambridge Crystallographic Data ... 2331-2339. Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F. Jr, Brice, M. D., Rodgers, ...

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 ]
... CA 92121-3752, USA. Eisenberg, D., Lüthy, R. & Bowie, J. U. (1997). VERIFY3D: assessment of protein models with three ... Errors in protein structures. Nature (London), 381, 272. Kleywegt, G. J. & Jones, T. A. (1996b). Efficient rebuilding of protein structures. Acta Cryst. D52, 829-832. Oldfield, T. J. (1992). SQUID: a program for the analysis and ...

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 ]
Output produced 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, with any unusual geometrical properties highlighted. The listing also provides summaries for the protein as a whole. Figs. 21.4.6.1 and 21.4.6.2 ...

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 ]
... influenced by the use of rotamer libraries. References Kleywegt, G. J. & Jones, T. A. (1996a). Phi/psi-chology: Ramachandran revisited. Structure, 4, 1395-1400. Kleywegt, G. J. & Jones, T. A. (1996b). Efficient rebuilding of protein structures. ... 832. Morris, A. L., MacArthur, M. W., Hutchinson, E. G. & Thornton, J. M. (1992). Stereochemical quality of protein structure ...

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 ]
... Peters, B. G., Kennard, O., Motherwell, W. D. S., Rodgers, J. R. & Watson, D. G. (1979). The Cambridge Crystallographic Data ... 400. Morris, A. L., MacArthur, M. W., Hutchinson, E. G. & Thornton, J. M. (1992). Stereochemical quality of protein structure coordinates. ...

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 ]
... symbols for the description of the conformation of polypeptide chains. J. Mol. Biol. 52, 1-17. International Tables for Crystallography (2012 ...

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 ]
... Addison-Wesley. Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F. Jr, Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). The ... Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542. Laskowski, R. A., MacArthur, ...

Protein-fold classification
Orengo, C. A. and Thornton, J. M.  International Tables for Crystallography (2012). Vol. F, ch. 23.1, pp. 749-751 [ doi:10.1107/97809553602060000890 ]
... Bernstein, F. C., Bryant, S. H., Koetzle, T. F. & Weng, J. (1987). Protein Data Bank. In Crystallographic Databases - Information Content ... Allen, G. Bergerhoff & R. Sievers, pp. 107-132. Artymiuk, P. J., Mitchell, E. M., Rice, D. W. & Willett, P. (1989). Searching techniques for databases of protein structures. J. Inf. Sci. 15, 287-298. Barton, G. J. (1997) ...

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