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Local error estimates dramatically improve the utility of homology models for solving crystal structures by molecular replacement.


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Type

Article

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Authors

Bunkóczi, Gábor 
Wallner, Björn 
Read, Randy J 

Abstract

Predicted structures submitted for CASP10 have been evaluated as molecular replacement models against the corresponding sets of structure factor amplitudes. It has been found that the log-likelihood gain score computed for each prediction correlates well with common structure quality indicators but is more sensitive when the accuracy of the models is high. In addition, it was observed that using coordinate error estimates submitted by predictors to weight the model can improve its utility in molecular replacement dramatically, and several groups have been identified who reliably provide accurate error estimates that could be used to extend the application of molecular replacement for low-homology cases.

Description

Keywords

Crystallography, X-Ray, Models, Molecular, Protein Conformation, Proteins, Reproducibility of Results, Research Design, Sequence Homology, Amino Acid

Journal Title

Structure

Conference Name

Journal ISSN

0969-2126
1878-4186

Volume Title

23

Publisher

Cell Press
Sponsorship
Wellcome Trust (082961/Z/07/Z)
Wellcome Trust (100140/Z/12/Z)
National Institute of General Medical Sciences (P01GM063210)
Support received from the NIH (grant P01GM063210), the Wellcome Trust (Principal Research Fellowship to R.J.R., grant 082961/Z/07/Z; Strategic Award to the Cambridge Institute for Medical Research), as well as from the Swedish Research Council (621-2012-5270), Swedish e-Science Research Center, and Carl Tryggers Stiftelse to B.W. is gratefully acknowledged.