Protein structural alignment is important for studying similarities between proteins. Various protein structural alignment tools have been developed for this task. These alignment tools have different characteristics and strategies on which they are based. In order to find out which structural alignment tool is the best for the application in hand and to develop better tools it is very important to classify the tools into groups based on these strategies and characteristics. In this research we have studied several protein structural alignment tools and categorized them based on several properties. This provides a basis and background work for the development of future structural alignment tools.
Typically the developers of a given structural alignment program test the program on a few pairs of proteins and comment on its comparison with other previously developed tools. Although there are a large number of alignment tools available, the tools have never been subjected to a comprehensive and critical comparative analysis on the basis of a common data set or test bench. The absence of such a common data set is the major reason for the lack of this analysis. In this research, we propose a benchmark data set to test any protein structural alignment program. This data set is composed of 221 protein pairs and is divided into 11 categories. We have tested all the online available structural alignment tools on this data set and analyzed their performance. On the basis of the alignment results we have computed overall rankings of these alignment tools using three different rating methods.