Welcome to OLIGAMI v2.00

OLIGAMI is a database of protein quaternary structures that can help us understand and interpret oligomer architecture at molecular interfaces. OLIGAMI utilizes a chain formula to report the oligomer chain composition of any biological complex and allows you quick access to the coordinate data you want through the SCOPe or CATH hierarchy and can provide information on soluble and membrane proteins separately using information from the Orientations of Proteins in Membranes (OPM) database. The oligomer interfaces are then classified based on their secondary structural features. You can browse oligomers based on our interface classifications. In the JSmol view of OLIGAMI, each oligomer subunit is color-coded so you can easily distinguish them.

Coordinate Files of the Biological Assembly of OLIGAMI

  • Individual chain names
    • So that each chain in JSmol view can be distinguished, each chain name is rewritten by its individual name.
  • Secondary structure definition
    • All secondary structures in OLIGAMI are recalculated with the program DSSP using new coordinate files with new chain names, and the secondary structural information is rewritten.

Chain Formula of OLIGAMI

  • Three types of chain formulas
    • The chain formula expresses the chain composition of any biological assembly. OLIGAMI has three types of chain formulas for every entry, which distinguish the chains based on their amino acid sequence, their family sections of the SCOPe hierarchy, and 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

  • Download a list of all chain formulas in OLIGAMI
    • OLIGAMI-CF-v2.0.txt

Interface classification of OLIGAMI

  • Secondary structure–based classification
    • We defined the seven interacting area types based on the fraction of each secondary structure for interface residues. Then, the interface class is defined based on two interacting area types that make contact with each other. The secondary structures have been defined using the program DSSP. Please see the "Interfaces" page for more detail.

External Databases

  • PDB : Jan. 2019
  • SCOPe : 2.07 release (Dec. 27, 2017)
  • CATH : v4.1.0
  • OPM : Feb. 13, 2017

Reference