Further performance comparison between PCalign and Ialign. When a method finds higher coverage with lower RMSD for a particular pair of interfaces compared, it is considered better for that case; with lower coverage and higher RMSD, it is considered worse. All cases of PCalign (plotted in green) outperforming Ialign (plotted in orange) and Ialign outperforming PCalign in the 185136 pairs compared are shown in the scatter plots and summarized in the bar plots. (A) In 50838 cases, PCalign is better than Ialign, when the chemical term in PC-score is turned on. (B) Ialign outperforms PCalign in 34087 cases in comparison. (C) PCalign has an odds ratio of 1.5 in finding a better structural alignment than Ialign. (D) When only geometrical property is considered in the scoring function, PCalign outperforms Ialign in 57639 cases. (E) Ialign is better than PCalign in 27790 cases. (F) PCalign outperforms Ialign with an odds ratio of 2.1 if only the physical environment of protein-protein interfaces is considered.