Protein Data Bank (PDB) Database

The Protein Data Bank (PDB) is a database for 3-D structural data of proteins and nucleic acids. The data is typically obtained by X-ray crystallography or NMR spectroscopy and is submitted by chemists from around the world, is released into the public domain, and can be accessed for free.

PDB files can be retrieved via the PDB website from within Spartan. Bound ligands can be extracted and associated with chemical function descriptors (designating hydrogen bonds, electrostatic interactions and hydrophobic regions) as well as the peptide/nucleotide base residues comprising the active site environment, and excluded volume centers (indicating the space occupied by the protein/nucleotide). A database of ~1250 small molecules bound to proteins/nucleotides in the PDB is included as part of Spartan Molecular Database and may be searched by substructure.