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. 2015 Feb 3;23(2):397-406.
doi: 10.1016/j.str.2014.11.020. Epub 2015 Jan 22.

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

Gábor Bunkóczi  1 , Björn Wallner  2 , Randy J Read  3
Affiliations

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

Gábor Bunkóczi et al. Structure. .

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.

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Figures

Figure 1
Figure 1
Typical LLG versus GDT_TS Scatter Plots Observed for Targets (A) Target TR705 contains two domains and refinement of one of these was requested. If the second domain is not taken into account in the likelihood calculations, the black curve is obtained, which shows no correlation between the two scores. However, by taking the contribution from the second domain into account (grey curve), a clear correlation is obtained (for scores shown, the contribution of the second domain alone is subtracted for the plot). ASU, asymmetric unit. (B) Uninformative LLG plot for target T0653 with all models falling into the low accuracy zone. (C) Very sensitive LLG plot for target T0717, domain 2 (taking the unpredicted domain 1 into account). Predictors have managed to model residues Val67 to Gly119 (out of 166 residues) very accurately, and this gives a clear signal in scoring with the 1.9 Å X-ray data. For the “outlier” models above GDT_TS = 35, the accuracy of the named residue segment is comparable with that of the rest of the structure. (D) Atypically small signal observed for target T0704.
Figure 2
Figure 2
Average Z Scores for Predictors Calculated with All Three B-Factor Schemes In the original scheme, the numbers appearing in the B-factor field were used as is; in the root mean square (Rms) scheme, these were converted into a B factor using Equation 1 and, in the constant scheme, these were set to a constant number.
Figure 3
Figure 3
Number of Targets Improved upon the Baseline Structure, Taking into Account All Three B-Factor Schemes
See this image and copyright information in PMC

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