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Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):303-12. doi: 10.1107/S0907444910051218. Epub 2011 Mar 18.

Improvement of molecular-replacement models with Sculptor.

Author information

1
CIMR Haematology, University of Cambridge, Wellcome Trust/MRC Building, Cambridge, England.

Abstract

In molecular replacement, the quality of models can be improved by transferring information contained in sequence alignment to the template structure. A family of algorithms has been developed that make use of the sequence-similarity score calculated from residue-substitution scores smoothed over nearby residues to delete or downweight parts of the model that are unreliable. These algorithms have been implemented in the program Sculptor, together with well established methods that are in common use for model improvement. An analysis of the new algorithms has been performed by studying the effect of algorithm parameters on the quality of models. Benchmarking against existing techniques shows that models from Sculptor compare favourably, especially if the alignment is unreliable. Carrying out multiple trials using alternative models created from the same structure but using different algorithm parameters can significantly improve the success rate.

PMID:
21460448
PMCID:
PMC3069745
DOI:
10.1107/S0907444910051218
[Indexed for MEDLINE]
Free PMC Article

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