Nugent, T; Cozzetto, D; Jones, DT; (2013) Evaluation of predictions in the CASP10 model refinement category. Proteins , 82 (Issue ) pp. 98-111. 10.1002/prot.24377.

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Abstract

Here we report on the assessment results of the third experiment to evaluate the state-of-the-art in protein model refinement, where participants were invited to improve the accuracy of initial protein models for twenty-seven targets. Using an array of complementary evaluation measures, we find that five groups performed better than the naïve (null) method - a marked improvement over CASP9, although only three were significantly better. The leading groups also demonstrated the ability to consistently improve both backbone and side-chain positioning, while other groups reliably enhanced other aspects of protein physicality. The top-ranked group succeeded in improving the backbone in almost 90% of targets, suggesting a strategy that for the first time in CASP refinement is successful in a clear majority of cases. A number of issues remain unsolved: the majority of groups still fail to improve the quality of the starting models; even successful groups were only able to make modest improvements; and no prediction was more similar to the native structure than to the starting model. Successful refinement attempts also often go unrecognized, as suggested by the relatively larger improvements when predictions not submitted as model 1 are also considered. © Proteins 2013;. © 2013 Wiley Periodicals, Inc.

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