Evaluation of predictions in the CASP10 model refinement category
By Timothy Nugent, Domenico Cozzetto, David T. Jones. 2013
116 citations recorded by the source corpus.
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 27 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 conformation 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 are only able to make modest improvements; and no prediction is 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 2014; 82(Suppl 2):98–111. © 2013 Wiley Periodicals, Inc.
Subfields: Materials Chemistry, Molecular Biology
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Materials Chemistry
- Andriy Kryshtafovych
- Torsten Schwede
- Krzysztof Fidelis
- John Moult
- Yang Zhang
- Michael Feig
- Bohdan Monastyrskyy
- Marco Biasini
In Molecular Biology
- Andriy Kryshtafovych
- Torsten Schwede
- Krzysztof Fidelis
- Yang Zhang
- John Moult
- Bohdan Monastyrskyy
- Michael Feig
- Anna Tramontano
Citations in the corpus
- Critical Assessment of Methods of Protein Structure Prediction (CASP) – Round XIII (2019, background): “A few CASPs ago, success with minor repositioning of secondary structure elements became common, for example.(27) More recently, and especially in this CASP,(26) larger range corrections (eg, a 7.”
- CASP10 results compared to those of previous CASP experiments (2013, methodology): “In CASP10, as described in a companion article,18 for the first time a refinement method succeeded in consistently improving the accuracy of every target, albeit by a small average amount.”
- Challenging the state-of-the-art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10 (2014, background): “…themselves, techniques for their assessment also have to evolve to better reflect the issues important for structural biology research.8, 9,73,74 The examples presented in this article highlight a series of reoccurring themes that appear to be challenging for current methods and might…”
- Assessment of the model refinement category in CASP12 (2017, methodology): “1,7,31,32 Refinement targets are selected from amongst the main challenge targets.”
- Computational protein structure refinement: Almost there, yet still so far to go (2017, background): “46,63,66 This may be useful information since the quality of initial models can be assessed with some degree of certainty.”