PROTEIN STRUCTURE ALIGNMENT ALGORITHM STUDIES

Abstract

Protein Structure Alignment is one of the major areas in Structure biology. Many techniques and algorithms proposed by various authors do exist. For example: DALI, MaxSub, Combinatorial Extension, TM align, TMscore. But, none of them is perfect. One technique take one feature into account and other technique takes other features into account based on the understanding of the authors. For example some compare the distance matrices of both the proteins and give some similarity measure based on the similarity of the values and then they do some scoring. Some are based on the defining equivalences and doing superposition and calculating the number of Calpha atoms whose distances are below the threshold. Others calculate the secondary state structure of each and every residue and then proceed further for the alignment procedure. Here, I have done studies of the various existing algorithms and I have proposed a new idea for the protein-protein structure alignment. My implementation of algorithm idea for protein structure alignment is exciting and studying this new algorithm provides new insights in the field of protein protein structure alignment. My algorithm studies are based on the modification of existing TM-score .My algorithm takes into account contribution from each and every atom constituting the structure. Earlier algorithm only takes one atom as representation of the protein residue and ignores every other atom. Here, I have developed the weightage scheme which will allow us to take the contribution from every atom. Allowing taking contribution from each and every atom is helpful to us to have real picture of the alignment, which was not clear to us when we blindly take only one atom as the representation of the whole residue. Also, I have compared the results of the new algorithm with the existing one.