A Protein Structure Retrieval System Using 3D LRA

Many structural comparison methods of proteins have been proposed [2,3,4,5]. Among them, distance matrices, approximation of structure, and vector representation are the most commonly used. The distance matrices, also called distance plots or distance maps, contain all the pair-wise distances between alpha-carbon atoms, i.e. Cα atoms of each residue [3]. A matrix is a twodimensional (2D) representation of a three-dimensional (3D) structure. This representation has critical weak points in terms of computational complexity and sensitivity to errors in the global optimization of alignment. In recent research work, this representation was improved by taking into consideration average conformations, the average coordinate of a small number of contiguous residues, instead of alpha-carbon atoms [4]. The improved representation is an approximation of the protein structure for a quick comparison. It overcomes the weak points on sensitivity to errors and computational complexity.