Local error estimates dramatically improve the utility of homology models for solving crystal structures by molecular replacement.
Bottom Line: 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.
Affiliation: Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK.Show MeSH
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Mentions: LLG scores were calculated for all predictions submitted for CASP10 targets that were determined by X-ray crystallography and for which the measured X-ray diffraction amplitudes were available. The relationship with the GDT_TS score was examined on scatter plots (Figure 1). For the majority of cases, the LLG score showed a clear functional relationship with the GDT_TS score. At GDT_TS < 40–50, the LLG scores were almost constant (average Spearman correlation coefficient for segment GDT_TS ≤ 50, 36%); they started to increase slowly for GDT_TS values above 50–60 and then very rapidly for GDT_TS > 80 (average Spearman correlation coefficient for segment GDT_TS > 50, 71%), although some deviations have also been observed (Figures 1C and 1D). This suggests that the LLG score cannot discriminate among predictions with large errors but can accurately rank good-quality predictions.
Affiliation: Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK.