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Table 3 Average per-target correlation and loss for DeepQA and other top performing single-model QA methods on CASP11. The table is ranked based on the average per-target loss on stage two of CASP11. P-value of Wilcoxon signed ranked sum test* between DeepQA and other methods is also included in the table

From: DeepQA: improving the estimation of single protein model quality with deep belief networks

QA methods Corr. on stage 1 /P-Value Loss on stage 1 /P-Value Corr. on stage 2 /P-Value Loss on stage 2 /P-Value
DeepQA 0.64/- 0.09/- 0.42/- 0.06/-
ProQ2 0.64/4.80E-01 0.09/8.32E-01 0.37/2.84E-03 0.06/9.95E-01
Qprob 0.63/8.08E-01 0.10/9.38E-01 0.38/8.63E-03 0.07/7.12E-01
VoroMQA 0.56/1.60E-04 0.11/2.73E-01 0.40/2.57E-01 0.07/9.14E-01
ProQ2-refine 0.65/6.08E-02 0.09/9.17E-01 0.37/4.71E-03 0.07/4.86E-01
Wang_SVM 0.66/5.49E-02 0.11/7.98E-02 0.36/1.54E-02 0.09/4.91E-02
raghavagps-qaspro 0.35/3.79E-13 0.16/1.87E-04 0.22/1.92E-10 0.09/1.02E-03
Wang_deep_2 0.63/9.98E-01 0.12/7.18E-02 0.31/2.16E-06 0.09/8.22E-03
Wang_deep_1 0.61/3.06E-01 0.13/1.64E-03 0.30/5.93E-06 0.09/5.00E-03
Wang_deep_3 0.63/7.18E-02 0.12/3.15E-02 0.30/8.22E-03 0.09/8.22E-03
FUSION 0.10/8.43E-14 0.15/9.78E-04 0.05/1.81E-13 0.11/2.83E-07
RFMQA 0.54/1.61E-01 0.12/8.74E-01 0.29/3.80E-03 0.08/3.80E-03
ProQ3 0.65/1.62E-01 0.07/3.60E-02 0.38/4.44E-01 0.06/4.09E-01
ResQ* 0.67/- 0.05/- 0.58/- 0.09/-
ModFOLDclust2 0.74/3.96E-05 0.05/6.34E-04 0.56/1.80E-03 0.07/1.41E-01
Mean 0.57 0.11 0.33 0.08
  1. * The Wilcoxon signed ranked sum test was performed on the correlation and loss of targets between each method against DeepQA
  2. * ResQ was evaluated on 54 targets in CASP11, the local quality scores were converted into global quality score by equation \( Global=\frac{1}{L}{\sum}_{i=1}^L\frac{1}{1+{\left(\frac{Loca{l}_i}{5}\right)}^2} \). More detailed results can be found in Additional file 1: Table S4