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Bioinformatics 2005 21(Suppl 2):ii72-ii76; doi:10.1093/bioinformatics/bti1112
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oxfordjournals.org

Evaluating the usefulness of protein structure models for molecular replacement

Alejandro Giorgetti 1,{dagger}, Domenico Raimondo 1,{dagger}, Adriana Erica Miele 1 and Anna Tramontano 1,2,*

1Department of Biochemical Sciences, University of Rome ‘La Sapienza’ 00185 Rome, Italy
2Istituto Pasteur—Fondazione Cenci Bolognetti, University of Rome ‘La Sapienza’ 00185 Rome, Italy

*To whom correspondence should be addressed.

Motivation: We investigate the relationship between the quality of models of protein structure and their usefulness as search models in molecular replacement, a widely used method to experimentally determine protein structures by X-ray crystallography.

Results: We used the available models submitted to the Critical Assessment of Techniques for Protein Structure Prediction to verify in which cases they can be automatically used as search templates for molecular replacement. Our results show that there is a correlation between the quality of the models and their suitability for molecular replacement but that the traditional method of relying on sequence identity between the model and the template used to build it is not diagnostic for the success of the procedure.

Availability: Additional data are available at http://cassandra.bio.uniroma1.it/mr-results-casp.html

Contact: anna.tramontano{at}uniroma1.it


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