Table 1.

Pearson’s correlation coefficient for different input features

Training data	Pearson’s correlation
ProQ	0.54 (±0.006)
Retrained ProQ (Base)	0.55 (±0.006)
Atom	0.43 (±0.006)
Residue	0.27 (±0.008)
Surface	0.47 (±0.006)
Residue + Profile Weighting	0.32 (±0.007)
Surface + Profile Weighting	0.51 (±0.006)
Base + Global Surface Area Prediction	0.65 (±0.005)
Base + Global Secondary Structure Pred.	0.65 (±0.005)
Base + Profile Weighting	0.62 (±0.005)
Base + Local Surface Area Prediction	0.58 (±0.005)
Base + Local Secondary Structure Pred.	0.58 (±0.005)
Base + Information per position (Conservation)	0.56 (±0.006)
All Combined (ProQ2)	0.71 (±0.004)

Overall Pearson’s correlation coefficient, for different input features, benchmarked using cross-validation on the CASP7 data set. (Errors correspond to 99.9% confidence intervals).