Comparative Analysis of Three Efficient Approaches for Retrieving Protein 3D Structures

In this paper, comparative analysis is presented of our three 3D structure-based approaches for the efficient retrieval of protein molecules. All approaches rely on the 3D structure of the proteins. In the first approach, the Spherical Trace Transform is applied to protein 3D structures in order to produce geometry based descriptors. Additionally, some biological properties of the protein are taken, thus forming better integrated descriptor. In the second approach, some modification of the ray based descriptor is applied on the backbone of the protein molecule. In the third approach, wavelet transformation is applied on the distance matrix of the Calpha atoms which form the backbone of the protein. The SCOP database was used to evaluate the retrieval accuracy. We provide some experimental results of the retrieval accuracy of our three approaches. The results show that the ray based approach gives the best retrieval accuracy (97,5%), while it is simpler and faster than the other two approaches.