Evaluation of model refinement in CASP13. Issue 12 (20th August 2019)

• Record Type: Journal Article
• Authors: Read, Randy J.; Sammito, Massimo D.; Kryshtafovych, Andriy; Croll, Tristan I.
• Is Part Of: Proteins. Volume 87:Issue 12(2019)
• Page Start: 1249
• Page End: 1262
• Publication Date: 2019-08-20
• Subjects: CASP -- model refinement -- molecular replacement -- structure prediction; Proteins -- Periodicals; Proteins -- Periodicals; 572.6
• DOI: 10.1002/prot.25794
• Languages: English
• ISSNs: 0887-3585

Abstract

Abstract: 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.