3D Complex: A Structural Classification of Protein Complexes
Figure 2
Representing Protein Complexes as Graphs
(A) Each protein complex is transformed into a graph where nodes represent polypeptide chains and edges represent biological interfaces between the chains.
(B) All complexes are compared with each other using a customized graph-matching procedure. Complexes with the same graph topology are grouped to form the top level of the hierarchy, as shown by the green boxes. If, in addition, the subunit structures are related by their SCOP domain architectures, they are grouped at the second level, shown by the red boxes. Structures were rendered with VMD [51].