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ARP/wARP - automated model building and refinement
Lamzin, V. S., Perrakis, A. and Wilson, K. S.  International Tables for Crystallography (2012). Vol. F, ch. 18.8, pp. 525-528 [ doi:10.1107/97809553602060000862 ]
... demanding and highly subjective step, heavily dependent on the researcher's experience, has been largely substituted by automated procedures. Automated model ... proceed. ARP/wARP has built on two innovative concepts (Lamzin & Wilson, 1993, 1997; Perrakis et al., 1999). (1) It challenged ... of free atoms (Agarwal & Isaacs, 1977), as described by Lamzin & Wilson (1997), that have undefined chemical identity: these atoms are ...

Iterations
Lamzin, V. S., Perrakis, A. and Wilson, K. S.  International Tables for Crystallography (2012). Vol. F, Section 18.8.4, p. 528 [ doi:10.1107/97809553602060000862 ]
Iterations 18.8.4. Iterations Building protein chains or solvent with ARP/wARP proceeds in an iterative fashion. When the quality of the (partially built) model is sufficiently high, the phases improve overall and result in an enhanced electron density where a more accurate and more complete model may be built. An important ...

Solvent building
Lamzin, V. S., Perrakis, A. and Wilson, K. S.  International Tables for Crystallography (2012). Vol. F, Section 18.8.3.5, pp. 527-528 [ doi:10.1107/97809553602060000862 ]
Solvent building 18.8.3.5. Solvent building In this application, the protein model (together with bound metals, ligands or nucleic acids) is not rebuilt during refinement. Instead, only the solvent structure is continuously updated. Since ordered solvent in a typical crystal structure comprises about 10% of the model, improvement of solvent indirectly improves ...
     [more results from section 18.8.3 in volume F]

Free-atom and hybrid models
Lamzin, V. S., Perrakis, A. and Wilson, K. S.  International Tables for Crystallography (2012). Vol. F, Section 18.8.2, pp. 525-526 [ doi:10.1107/97809553602060000862 ]
... of free atoms (Agarwal & Isaacs, 1977), as described by Lamzin & Wilson (1997), that have undefined chemical identity: these atoms are chosen ... Proc. Natl Acad. Sci. USA, 74, 2835-2839. Lamzin, V. S. & Wilson, K. S. (1997). Automated refinement for protein crystallography. ...

Refinement and model building are two parts of modelling a structure
Lamzin, V. S., Perrakis, A. and Wilson, K. S.  International Tables for Crystallography (2012). Vol. F, Section 18.8.1, p. 525 [ doi:10.1107/97809553602060000862 ]
... proceed. ARP/wARP has built on two innovative concepts (Lamzin & Wilson, 1993, 1997; Perrakis et al., 1999). (1) It challenged ... the quality of the initial phase estimates. References Lamzin, V. S. & Wilson, K. S. (1993). Automated refinement of protein models. ...

Applicability and requirements
Lamzin, V. S., Perrakis, A. and Wilson, K. S.  International Tables for Crystallography (2012). Vol. F, Section 18.8.5, p. 528 [ doi:10.1107/97809553602060000862 ]
... quality. Recent advances in refinement using experimental phasing information (Skubák et al., 2009) proved essential for successful automated model building ... and are likely to change in the future. References Skubák, P., Murshudov, G. & Pannu, N. S. (2009). A multivariate likelihood SIRAS function for phasing ...

Practical strategies
Dauter, Z., Murshudov, G. N. and Wilson, K. S.  International Tables for Crystallography (2012). Vol. F, Section 18.4.8, p. 496 [ doi:10.1107/97809553602060000858 ]
... Methods Enzymol. 368, 288-337. Dauter, Z., Sieker, L. C. & Wilson, K. S. (1992). Refinement of rubredoxin from Desulfovibrio vulgaris at ...

Relation to biological chemistry
Dauter, Z., Murshudov, G. N. and Wilson, K. S.  International Tables for Crystallography (2012). Vol. F, Section 18.4.7, pp. 495-496 [ doi:10.1107/97809553602060000858 ]
... atomic resolution structures. J. Mol. Biol. 276, 417-436. Popper, K. R. (1959). The Logic of Scientific Discovery. London: Hutchinson. ...

Quality assessment of the model
Dauter, Z., Murshudov, G. N. and Wilson, K. S.  International Tables for Crystallography (2012). Vol. F, Section 18.4.6, p. 495 [ doi:10.1107/97809553602060000858 ]
... amino acids and peptides in the Cambridge Crystallographic Data Centre's small-molecule crystal structure database (Allen et al., 1979). ... A., Shapovalov, M. V., Dunbrack, R. L. Jr & Berkholz, D. S. (2008). A forward-looking suggestion for resolving the stereochemical ... functions. Acta Cryst. D64, 335-336. Allen, F. H., Bellard, S., Brice, M. D., Cartwright, B. A., Doubleday, A., Higgs, ...

Deformation density
Dauter, Z., Murshudov, G. N. and Wilson, K. S.  International Tables for Crystallography (2012). Vol. F, Section 18.4.5.8, pp. 494-495 [ doi:10.1107/97809553602060000858 ]
... and protein structures. Acta Cryst. D54, 1306-1318. Lamzin, V. S., Morris, R. J., Dauter, Z., Wilson, K. S. & Teeter, M. M. (1999). Experimental observation of ...
     [more results from section 18.4.5 in volume F]

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