A bipartite graph matching framework for finding correspondences between structural elements in two proteins

A protein molecule consists one or more chains of amino acid sequences that fold into a complex three-dimensional structure. A protein's functions are often determined by its 3D structure, and so comparing the similarity of 3D structures between proteins is an important problem. To accomplish such comparison, one must align two proteins properly with rotation and translation in 3D space. Finding the correspondences between structural elements in the two proteins is the key step in many protein structure alignment algorithms. We introduce a new graph theoretic framework based on bipartite graph matching for finding sufficiently good correspondences. It is capable of providing both sequence-dependent and sequence-independent correspondences. It is a general framework for pair-wise matching of atoms, amino acids residues or secondary structure elements.