P212121

Protein + Small Molecule Databases:
1) HIC-Up freely accessible resource for structural biologists who are dealing with small molecules
2) PRODRG2 a server for high throughput crystallography of protein-ligand complexes
3) ValLigURL protein ligand comparison and validation (post)
4) BindingDB experimentally determined protein-ligand binding affinities (Ki, IC50, ITC, post)
5) DBGET integrated database retrieval system for major biological databases
6) Ligand Expo provides chemical and structural information about small molecules within the structure entries of the PDB
7) LPDB selection of complexes based on various properties of receptors and ligands for the design and parametrization of new scoring functions or to assess and improve existing ones
MSDChem provides web access to the “Chemical Component Dictionary” of the wwPDB as this is loaded in the PDBe database at EBI.
9) PISA tool for the exploration of macromolecular (protein, DNA/RNA and ligand) interfaces
10) Relibase search, retrieval and analysis system for protein-ligand complex structures (registration required)
11) RESID collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications
12) 15 Carbohydrate Databases

Small Molecule Databases:
1) CSD world repository of small molecule crystal structures
2) ChemDB nearly 5M commercially available small molecules
3) COD search over 88k small molecules for free
4) A La Mode building models of ligand & monomer molecular components (nucleic acids)
5) NCI Open Database 250k+ compounds searchable by name, CAS numbers, formula, name, etc.
6) ZINC free database of commercially-available compounds for virtual screening
7) ICSD inorganic crystal structure database (dead)