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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 ]
... of the model itself, without reference to the experimental data (MacArthur et al., 1994; Laskowski et al., 1998). Here we ... Reading, MA: Addison-Wesley. Allen, F. H., Bellard, S., Brice, M. D., Cartwright, B. A., Doubleday, A., Higgs, H., Hummelink, T., Hummelink-Peters, B. G., Kennard, O., Motherwell, W. D. S., Rodgers, J. R. & Watson, D. G. (1979) ...

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 ]
... protein structures. Acta Cryst. D52, 829-832. Morris, A. L., MacArthur, M. W., Hutchinson, E. G. & Thornton, J. M. (1992). Stereochemical ...

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 ]
... in the structure. References Allen, F. H., Bellard, S., Brice, M. D., Cartwright, B. A., Doubleday, A., Higgs, H., Hummelink, T., Hummelink-Peters, B. G., Kennard, O., Motherwell, W. D. S., Rodgers, J. R. & Watson, D. G. (1979). ... structure refinement. Acta Cryst. A47, 392-400. Morris, A. L., MacArthur, M. W., Hutchinson, E. G. & Thornton, J. M. (1992) ...

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 file, relabelling certain side-chain atoms according to the IUPAC naming conventions (IUPAC-IUB Commission on Biochemical Nomenclature ...

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 ]
... of the model itself, without reference to the experimental data (MacArthur et al., 1994; Laskowski et al., 1998). Here we ... F., Williams, G. J. B., Meyer, E. F. Jr, Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). The Protein Data Bank: a computer-based ...

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 ]
... three-dimensional profiles. Methods Enzymol. 277, 396-404. Hooft, R. W. W., Sander, C., Vriend, G. & Abola, E. E. (1996). Errors ...

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