Benchmarking deep networks for predicting residue-specific quality of individual protein models in CASP11

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 SVM with deep networks works well in terms of certain measurements.