Benchmarking Deep Networks for Predicting Residue-Specific Quality of Individual Protein Models in CASP11

Scientific Reports
Tong LiuZheng Wang

Abstract

Quality assessment of a protein model is to predict the absolute or relative quality of a protein model using computational methods before the native structure is available. Single-model methods only need one model as input and can predict the absolute residue-specific quality of an individual model. Here, we have developed four novel single-model methods (Wang_deep_1, Wang_deep_2, Wang_deep_3, and Wang_SVM) based on stacked denoising autoencoders (SdAs) and support vector machines (SVMs). We evaluated these four methods along with six other methods participating in CASP11 at the global and local levels using Pearson's correlation coefficients and ROC analysis. As for residue-specific quality assessment, our four methods achieved better performance than most of the six other CASP11 methods in distinguishing the reliably modeled residues from the unreliable measured by ROC analysis; and our SdA-based method Wang_deep_1 has achieved the highest accuracy, 0.77, compared to SVM-based methods and our ensemble of an SVM and SdAs. However, we found that Wang_deep_2 and Wang_deep_3, both based on an ensemble of multiple SdAs and an SVM, performed slightly better than Wang_deep_1 in terms of ROC analysis, indicating that integrating an ...Continue Reading

References

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Citations

Aug 18, 2016·Scientific Reports·Xiaoyang JingQiwen Dong
Oct 5, 2016·Scientific Reports·Karolis UzielaArne Elofsson
Mar 7, 2017·Proteins·Kliment Olechnovič, Česlovas Venclovas
Aug 5, 2017·Acta Crystallographica. Section D, Structural Biology·Su Datt LamChristine Orengo
May 1, 2017·Wiley Interdisciplinary Reviews. Computational Molecular Science·Michael Feig
Mar 3, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Kazi Lutful KabirAmarda Shehu
Mar 16, 2019·BMC Bioinformatics·Joseph LuttrellZheng Wang
Jan 6, 2017·Bioinformatics·Karolis UzielaArne Elofsson
Apr 23, 2020·Biomolecules·Jiarui Chen, Shirley W I Siu

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Methods Mentioned

BETA
X-ray

Software Mentioned

Theano
Wang
NNcon
CLUSTER
deep
Light
Pro
ProQ2
PSI
MULTICOM

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