A Flexible Algorithm for Pairwise Protein Structure Alignment

We develop a new algorithm for the pairwise protein structure alignment. Our algorithm has two phases. The first phase aligns all the possible local regions between two proteins. Each local region of a protein consists of a series of consecutive Cα atoms in the backbone of the protein. The second phase derives a global rigid body transformation that combines some aligned local regions to achieve a global alignment and make it as large as possible. Our main technical contribution is a new algorithm for the second phase, finding the transformation for the global alignment. The alignment accuracy measured by RMSD is adjustable by the user. The experiments show that its performance is better than two well known existing algorithms (DaliLite [5] and CE [9]).