As the sizes of three-dimensional (3D) protein structure databases are growing rapidly nowadays, exhaustive database searching, in which a 3D query structure is compared to each and every structure in the database, becomes inefficient. We propose a rapid 3D protein structure retrieval system named ProtDex2, in which we adopt the techniques used in information retrieval systems in order to perform rapid database searching without having access to every 3D structure in the database. The retrieval process is based on the inverted-file index constructed on the feature vectors of the relationships between the secondary structure elements (SSEs) of all the 3D protein structures in the database. ProtDex2 is a significant improvement, both in terms of speed and accuracy, upon its predecessor system, ProtDex.