A Study on Tools and Algorithms for 3-D Protein Structures Alignment and Comparison

Abstract

Since protein structure is well conserved over evolutionary time, it therefore provides the opportunity to recognize homology that is undetectable by sequence comparison, and it represents a powerful means of discovering functions. In addition, the three-dimensional structure of a protein can yield direct insight into its molecular mechanism. Currently, there are several techniques available in attempting to find the optimal alignment of shared structural motifs between two proteins. In this paper, we propose novel distance/similarity measurements and algorithms for pairwise alignment of protein structures. Methods of locating suitable isometric transformations of one structure, and align it to the other are addressed. Our methods allow sequence gaps of any length, reversal of chain direction, and free topological connectivity of aligned segments. Sequential connectivity can be imposed as an option. The method is fully automatic to identify structural resemblances and common structural cores accurately and sensitively, even in the presence of geometrical distortions