Local Error Estimates Dramatically Improve the Utility of Homology Models for Solving Crystal Structures by Molecular Replacement

By G. Bunkoczi, Björn Wallner, Randy J. Read. 2015

16 citations recorded by the source corpus.

Summary 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.

Subfields: Infectious Diseases, Molecular Biology, Oncology, Computational Biology & Bioinformatics

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In Infectious Diseases

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Citations in the corpus

Evaluation of template-based modeling in CASP13 (2019, methodology): “As suggested at the time of the CASP7 evaluation, 6 and as demonstrated in tests with models from CASP10, 33 the use of error estimates to inflate local B-factors of models, and thereby downweight the contributions of unreliable segments of the model at higher resolution, can dramatically increase…”
Using iterative fragment assembly and progressive sequence truncation to facilitate phasing and crystal structure determination of distantly related proteins. (2016, methodology): “Most recently, it was shown that B factors based on coordinate-error estimation can improve signal to noise such that weighted search models of low quality give a better signal than analogous unweighted high-quality models (Bunkóczi et al., 2015).”
Protein homology model refinement by large-scale energy optimization (2018, background): “Refinement improved the MR log likelihood gain (LLG) (21) by greater than 15 units for 8 of 10 CASP targets for which diffraction data were available (SI Appendix, Table S3).”
On the application of the expected log-likelihood gain to decision making in molecular replacement (2018, unknown): “D74, 245–255 Read, 2011; Bunkóczi et al., 2015).”