Proteins Structure Function and BioinformaticsBioinformaticsPeer-reviewed journal article
Methods For Estimation Of Model Accuracy In CASP12
Arne ElofssoniD, Keehyoung JooiD, Chen KeasariD, Jooyoung LeeiD, Ali H. A. Maghrabi, Balachandran ManavalaniD, Liam James McGuffiniD, David Menéndez HurtadoiD, Claudio MirabelloiD, Robert Pilstål, Tomer SidiiD, Karolis UzielaiD, Björn WallneriD
Abstract
Methods for reliably estimating the quality of 3D models of proteins are essential drivers for the wide adoption and serious acceptance of protein structure predictions by life scientists. In this paper, the most successful groups in CASP12 describe their latest methods for Estimates of Model Accuracy (EMA). We show that pure single model accuracy estimation methods has shown clear progress since CASP11; the three top methods (MESHI, ProQ3, SVMQA) all perform better than the top method of CASP11 (ProQ2). The pure single model accuracy estimation methods outperform quasi-single (ModFOLD6 variations) and consensus methods (Pcons, ModFOLDclust2, Pcomb-domain and Wallner) in model selection, but are still not as good as those methods in absolute model quality estimation and predictions of local quality. Finally, we show that when using contact based model quality measures (CAD, 1DDT) the single model quality methods perform relatively better.
- Citations
- 34
- FWCI
- 2.57
- Field percentile
- top 9%
Reproducibility ledger
Nobody has reported trying to reproduce this paper yet. Did you replicate an experiment or run the code? Your report saves the next lab a week.
Sign in to file a reproducibility report.
Related papers
- Improved protein model quality assessments by changing the target function
Karolis Uziela, David Menéndez Hurtado, … Arne Elofsson·Proteins Structure Function and BioinformaticsPeer-reviewed·Mar 9, 2018
- Combining pairwise structural similarity and deep learning interface contact prediction to estimate protein complex model accuracy in CASP15
Jianlin Jack Cheng, Raj S. Roy, … Zhiye Guo·bioRxiv·Mar 8, 2023
- Highly Accurate Estimation of the Fold Accuracy of Protein Structural Models
Lei Xie, Enjia Ye, … Guijun Zhang·bioRxiv·May 13, 2026
- Protein model accuracy estimation empowered by deep learning and inter-residue distance prediction in CASP14
Xiao Chen, Jian Liu, … Jianlin Jack Cheng·Scientific ReportsPeer-reviewed·May 25, 2021
- Improved protein model quality assessment by integrating sequential and pairwise features using deep learning
Xiaoyang Jing, Jinbo Xu·BioinformaticsPeer-reviewed·Dec 1, 2020
- DISTEMA: distance map-based estimation of single protein model accuracy with attentive 2D convolutional neural network
Xiao Chen, Jianlin Jack Cheng·BMC BioinformaticsPeer-reviewed·Mar 1, 2022