Improved estimates of coordinate error for molecular replacement
By R. Oeffner, G. Bunkoczi, A. McCoy, Randy J. Read. 2013
39 citations recorded by the source corpus.
A function for estimating the effective root-mean-square deviation in coordinates between two proteins has been developed that depends on both the sequence identity and the size of the protein and is optimized for use with molecular replacement in Phaser. A top peak translation-function Z-score of over 8 is found to be a reliable metric of when molecular replacement has succeeded.
Subfields: Computational Mechanics, Materials Chemistry, Small Animals
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In Computational Mechanics
In Materials Chemistry
Citations in the corpus
- Local Error Estimates Dramatically Improve the Utility of Homology Models for Solving Crystal Structures by Molecular Replacement (2015, background): “Vrms Vrms is the error estimate for a model that gives the optimal (highest) LLG score (Oeffner et al., 2013).”
- On the application of the expected log-likelihood gain to decision making in molecular replacement (2018, methodology): “This reasoning is consistent with the results of database studies (Oeffner et al., 2013; McCoy et al., 2017), where a correct solution is equivalently indicated by a TFZ of 8 and an LLGI of 82 ( 60) in nonpolar space groups, a TFZ value that has long been associated with indicating a correct…”
- Using iterative fragment assembly and progressive sequence truncation to facilitate phasing and crystal structure determination of distantly related proteins. (2016, methodology): “A recent quantitative study showed that a TFZ of 8 indicates success for a nonpolar space group, while a TFZ of 6 is sufficient in a polar space group (Oeffner et al., 2013).”