Assessment of the model refinement category in CASP12.

Proteins
Ladislav HovanFrancesco Luigi Gervasio

Abstract

We here report on the assessment of the model refinement predictions submitted to the 12th Experiment on the Critical Assessment of Protein Structure Prediction (CASP12). This is the fifth refinement experiment since CASP8 (2008) and, as with the previous experiments, the predictors were invited to refine selected server models received in the regular (nonrefinement) stage of the CASP experiment. We assessed the submitted models using a combination of standard CASP measures. The coefficients for the linear combination of Z-scores (the CASP12 score) have been obtained by a machine learning algorithm trained on the results of visual inspection. We identified eight groups that improve both the backbone conformation and the side chain positioning for the majority of targets. Albeit the top methods adopted distinctively different approaches, their overall performance was almost indistinguishable, with each of them excelling in different scores or target subsets. What is more, there were a few novel approaches that, while doing worse than average in most cases, provided the best refinements for a few targets, showing significant latitude for further innovation in the field.

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Citations

Mar 7, 2018·Proceedings of the National Academy of Sciences of the United States of America·Hahnbeom ParkDavid Baker
Aug 12, 2018·Protein Science : a Publication of the Protein Society·Tianqi MaJianpeng Ma
May 12, 2019·International Journal of Molecular Sciences·Recep Adiyaman, Liam James McGuffin
Jul 22, 2019·Proteins·Hahnbeom ParkDavid Baker
Aug 1, 2019·Proteins·Randy J ReadTristan I Croll
Apr 20, 2019·Proceedings of the National Academy of Sciences of the United States of America·Xingcheng LinPeter G Wolynes
Apr 3, 2019·Physical Review. E·John D TreadoCorey S O'Hern
Jan 24, 2020·Computational and Structural Biotechnology Journal·Aleksandra E Badaczewska-DawidSebastian Kmiecik
Feb 11, 2021·Journal of Chemical Theory and Computation·Lim HeoMichael Feig
May 1, 2021·International Journal of Molecular Sciences·Cheng-Peng ZhouHong-Bin Shen
May 25, 2021·Computational and Structural Biotechnology Journal·Megan EgbertSandor Vajda
Jul 22, 2021·Proteins·Adam J SimpkinDaniel J Rigden
Jan 9, 2020·Journal of Chemical Theory and Computation·Stefano PianaDavid E Shaw
Sep 1, 2021·Proteins·Andriy KryshtafovychUNKNOWN CASP-COVID participants

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