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Evaluation of predictions in the CASP10 model refinement category.

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. Green open access

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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.

Type: Article
Title: Evaluation of predictions in the CASP10 model refinement category.
Open access status: An open access version is available from UCL Discovery
DOI: 10.1002/prot.24377
Publisher version: http://dx.doi.org/10.1002/prot.24377
Additional information: Copyright © 2013 Wiley Periodicals, Inc. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
Keywords: CASP, model quality evaluation, protein model refinement, protein structure prediction, template-based modelling
UCL classification: UCL
UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > UCL BEAMS
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science > Dept of Computer Science
URI: https://discovery.ucl.ac.uk/id/eprint/1405003
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