SATIS: Atom typing from chemical connectivity

SATIS (simple atom type information system) is a protocol for the definition and automatic assignment of atom types and the classification of atoms according to their covalent connectivity. Its distinctive feature is that no bond type information is involved. Rather, the classification of each atom is based on a connectivity code describing the atom and its covalent partners. It is particularly useful when handling coordinate-based molecular representations with no bond order information, such as the PDB format. We survey the occurrence of the various connectivity codes in the 20 common amino acid residues in a sample of 304 different moieties from PDB protein-ligand complexes and also in a pseudo-random sample of 309 organic molecules from the CSD. We illustrate how connectivity codes can be grouped together to define atom types. We expect SATIS to be applicable to the derivation of atom types for statistical potentials, to the analysis of atomic interactions in structural databases, to studies of molecular similarity, and to the screening of virtual libraries in drug design.