Evaluation of model refinement in CASP13
By Randy J. Read, M. Sammito, Andriy Kryshtafovych, T. Croll. 2019
24 citations recorded by the source corpus.
Performance in the model refinement category of the 13th round of Critical Assessment of Structure Prediction (CASP13) is assessed, showing that some groups consistently improve most starting models whereas the majority of participants continue to degrade the starting model on average. Using the ranking formula developed for CASP12, it is shown that only 7 of 32 groups perform better than a “naïve predictor” who just submits the starting model. Common features in their approaches include a dependence on physics‐based force fields to judge alternative conformations and the use of molecular dynamics to relax models to local minima, usually with some restraints to prevent excessively large movements. In addition to the traditional CASP metrics that focus largely on the quality of the overall fold, alternative metrics are evaluated, including comparisons of the main‐chain and side‐chain torsion angles, and the utility of the models for solving crystal structures by the molecular replacement method. It is proposed that the introduction of these metrics, as well as consideration of the accuracy of coordinate error estimates, would improve the discrimination between good and very good models.
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
- Maya Topf
- Bohdan Monastyrskyy
- Anna Tramontano
In Molecular Biology
- Andriy Kryshtafovych
- Torsten Schwede
- Krzysztof Fidelis
- John Moult
- Yang Zhang
- Bohdan Monastyrskyy
- Maya Topf
- Anna Tramontano
Citations in the corpus
- Improved protein structure prediction using predicted interresidue orientations (2019, neutral): “Progress was also evident in protein structure refinement at CASP13 using energy guided refinement (9-11).”
- Critical Assessment of Methods of Protein Structure Prediction (CASP) – Round XIII (2019, background): “The most recent assessment provides partial insight into that phenomenon, with clear examples where the noninclusion of interactions with other protein domains or binding partners limits accuracy.(26) As will be apparent again later, the modeling field has now advanced to the point where there is a ”