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Table 1 Different datasets used in the study.

From: PocketMatch: A new algorithm to compare binding sites in protein structures

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