Proteins show a great variety of 3D conformations, which can be used to infer their evolutionary relationship and to classify them into more general groups, therefore protein structure alignment algorithms are very helpful for protein biologists. However, an accurate alignment algorithm itself may be insufficient for effective discovering of structural relationships among tens of thousands of proteins. Due to the exponentially increasing amount of protein structural data, a fast and accurate structure alignment tool is necessary to access protein classification and protein similarity search, however, the complexity of current alignment algorithms are usually too high to make a fully alignment-based classification and search practical.