Table 4. Comparison of sequence order-independent binding site alignments constructed by SiteEngine and eMatchSite for adenine-binding proteins from the SOIPPA dataset.
| Algorithm | Crystal structures | High-quality models | Moderate-quality models | |||
| RMSD | ΔRMSD a | RMSD | ΔRMSD a | RMSD | ΔRMSD a | |
| SiteEngine | 5.63±3.37 | 3.67±2.91 | 6.78±3.29 | 4.83±2.92 | 7.89±3.68 | 6.01±3.46 |
| eMatchSite | 4.81±2.62 | 2.85±2.40 | 5.21±2.55 | 3.26±2.33 | 5.32±2.48 | 3.44±2.22 |
The alignment accuracy is assessed by the average ±standard deviation ligand heavy-atom RMSD calculated upon the superposition of aligned binding residues.
a
ΔRMSD is calculated by subtracting from RMSD a ligand heavy-atom root-mean-square deviation upon the superposition of two ligands.