Non-Redundant Binding Site Database

A database of non-redundant binding sites was created from all the existing protein-ligand complexes from the PDB. Redundancy was reduced by ensuring that the best possible binding site for a given ligand is chosen (by taking into account the highest resolution structure) per fold of a protein. A unique scheme was developed to assign the BSCOP (Binding Site SCOP) for a given site, and only one ligand binding site per BSCOP was chosen. Care was taken to ensure only the biologically relevant ligands are present in the database. Following flow-chart describes the various steps sequentially involved in the creation of the database. Database is available for download.

Statistics of Database

Database of Non-Redundant binding sites consisted of 9036 ligands with 18,895 binding sites. Following graph shows the frequency of different ligand-binding sites that exits in the database. HEM was the ligand having the most number of binding sites in the database, followed by other biologically important co-factors like ADP, ATP, ANP, FAD and SAH.

 

The redundancy of the database was acheived by taking into the consideration the fold of the protein at the binding site. The association of ligands with protein folds were analyzed. Following graph reveals that TIM beta/alpha barrel has the most number of unique ligand associations which is expected because of the diverse function this fold is involved in. The next topmost hits observed are of Protein-kinase like fold and proteases which are probably pharamacolgical targets.

 

 

Download NR-Binding Site Database

  • PocketAnnotate_dabatabase_Oct24_2011.zip
  • Binding site SCOP (bSCOP) was assigned to 12417 binding sites successfully - successful_bscop_assigned_Oct24_2011.txt
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