MCQ4Structures is a tool for structural similarity computation based on molecule tertiary structure representation in torsional angle space. Although it has been primarily designed to work with RNA structures, MCQ4Structures can be also applied to proteins (however their representation is restricted to the backbone angles).
MCQ4Structures was created using Java technology. In order to use the software, one should have Java Runtime Environment 1.7 installed (JRE is freely available for download).
MCQ4Structures is available as a free Java Webstart application and can be downloaded from:
The source code, licensed under BSD, is hosted on GitHub