Background: Many proteins can change their conformations or interact with different partners to show different biological functions.But its difficult and expensive for experiments to verify which functions may be observed for a protein.It is believed that protein functions relate closely with their 3D structures.So it is possible to find new functions for a protein by comparing its 3D structure to all the other know protein 3D structures.If the structures of two low-homologous proteins are shown to be similar, the functions of them will be similar also.But the traditional 3D structure methods have many drawbacks.