Chemical databases

• ChEMBL. Curated database of small molecules. Includes interactions and functional effects of small molecules binding to their macromolecular targets, and series of drug discovery databases.
  

Protein-ligand complexes databases

• Binding MOAD (Mother Of All Database). Subset of the Protein Data Bank (PDB), containing a collection of well resolved protein crystal structures with clearly identified biologically relevant ligands annotated with experimentally determined binding data extracted from literature. Maintained by the university of Michigan.
  
• PDBbind. Collection of experimentally measured binding affinity data (Kd, Ki, and IC50) exclusively for the protein-ligand complexes available in the Protein Data Bank (PDB). All of the binding affinity data compiled in this database are cited from original references.
  
• AffinDB. Freely accessible database of affinities for protein-ligand complexes from the PDB.
  
• Protein Ligand Database (PLD). Collection of protein ligand complexes extracted fom the PDB along with biomolecular data, including binding energies, Tanimoto ligand similarity scores and protein sequence similarities of protein-ligand complexes. Maintained by the University of Cambridge.
  
• BindingDB. Public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules.
  
• Ki Database. Provides information on the abilities of drugs to interact with an expanding number of molecular targets. The Ki database serves as a data warehouse for published and internally-derived Ki, or affinity, values for a large number of drugs and drug candidates at an expanding number of G-protein coupled receptors, ion channels, transporters and enzymes. Currently 55472 Ki values. Maintained by the NIMH Psychoactive Drug Screening Program.
  
• SCORPIO. Free online repository of protein-ligand complexes which have been structurally resolved and thermodynamically characterised.
  
• PDSP. Psychoactive Drug Screening Program. Provides screening of novel psychoactive compounds for pharmacological and functional activity at cloned human or rodent CNS receptors, channels, and transporters. Assays, K_i,...
  
• BAPPL complexes set. 161 protein-ligand complexes with experimental and estimated binding free energies calculated with the BAPPL server.
  
• DNA Drug complex dataset. Dataset of DNA-drug complexes consisting of 16 minimized crystal structures and 34 model-built structures, along with experimental affinities, used to validate PreDDICTA.
  
• Binding Database. Public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules. Maintained by the Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute.
  
• Kuntz Protein Test Set. Set of 114 crystallographically determined protein-ligand structures used to test the docking program DOCK. Maintained by UCSF.