Skip to main content

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