Welcome to OLIGAMI v1.9

OLIGAMI is a database of chain formulas, which express the chain composition of the biological assembly. OLIGAMI allows you to browse soluble and membrane oligomers separately using information from the Orientations of Proteins in Membranes (OPM) database and to quickly access to the coordinate data you want through the SCOPe or CATH hierarchy. Then, you can compare the amino acid–based chain formula and the structure-based chain formulas. In the JSmol view of OLIGAMI, each oligomer subunit is color-coded so you can easily distinguish them.

Download a list of all chain formulas in OLIGAMI

Chain Formula of OLIGAMI

  • The chain formula expresses the chain composition of the biological assembly. OLIGAMI has three types of chain formulas for every entry that distinguish the chains by their amino acid sequences, by their family sections of the SCOPe hierarchy, and by their homology sections of the CATH hierarchy.

Examples of Chain Formulas

  • [A3][a] : Homo trimer with a short peptide
  • [AB](AB) : Hetero dimer with a double-stranded DNA
    • [ ] : Polypeptide --- [AB] : Protein, [ab] : Small peptide
    ( ) : Nucleic acid --- (AB) : DNA, (ab) : RNA

Coordinate Files of the Biological Assembly of OLIGAMI

  • Individual chain names
    • To be able to distinguish each chain in the JSmol view, each chain name is rewritten by its individual name.
  • Secondary structure definition
    • We recalculate secondary structures with the DSSP program using new coordinate files with new chain names and rewrite the secondary structural information.

External Databases

Reference