Table 1.
No. | Dataset | Initial Size | Remarks | Final set used in the study | |
Proteins | Sites | ||||
i | PDBBind | 1091 | One representative ligand of each type is considered in each protein; filtered to remove sites for small and covalently bound ligands; retained proteins common with the SCOP database | 786 | 893 |
ii | PDBBind | 1091 | Filtered to remove sites for small, covalently bound ligand and all suggested by Jackson and co-workers (10) to contribute to noise; considered sites for all ligand types for the remaining | 456 | 1146 |
iii | Curated dataset of CIT,MTX,MK1 and PGA | 27 | Ligands for varying sizes and types from PDBBind with multiple sites for a ligand in different proteins | 27 | 51 |
iv | Tetramer | 3768 | Multiple sites for each ligand in the same protein; filtered to remove small and covalently bound ligands | 1525 | 11301 |