title: Pairwise protein structure alignment based on an orientation-independent backbone representation.
abstract: Determining structural similarities between proteins is an important problem since it can help identify functional and evolutionary relationships. In this paper, an algorithm is proposed to align two protein structures. Given the protein backbones, the algorithm finds a rigid motion of one backbone onto the other such that large substructures are matched. The algorithm uses a representation of the backbones that is independent of their relative orientations in space and applies dynamic programming to this representation to compute an initial alignment, which is then refined iteratively. Experiments indicate that the algorithm is competitive with two well-known algorithms, namely DALI and LOCK.
authors.affiliation: Department of Computer Science & Engineering, University of Minnesota, Minneapolis, MN 55455, USA. jieping@cs.umn.edu
authors.forename: Jieping
authors.initials: J
authors.lastname: Ye
authors.forename: Ravi
authors.initials: R
authors.lastname: Janardan
authors.forename: Songtao
authors.initials: S
authors.lastname: Liu
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011506:Proteins / Q000032:analysis / Q000737:chemistry* / Q000145:classification*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid
chemical_list: D011506:Proteins