title: Iterative non-sequential protein structural alignment.
abstract: Structural similarity between proteins gives us insights on the evolutionary relationship between proteins which have low sequence similarity. In this paper, we present a novel approach called STSA for non-sequential pair-wise structural alignment. Starting from an initial alignment, our approach iterates over a two-step process, a superposition step and an alignment step, until convergence. Given two superposed structures, we propose a novel greedy algorithm to construct both sequential and non-sequential alignments. The quality of STSA alignments is evident in the high agreement it has with the reference alignments in the challenging-to-align RPIC set. Moreover, on a dataset of 4410 protein pairs selected from the CATH database, STSA has a high sensitivity and high specificity values and is competitive with state-of-the-art alignment methods and gives longer alignments with lower rmsd. The STSA software along with the data sets will be made available on line at http://www.cs.rpi.edu/-zaki/software/STSA.
authors.affiliation: Computer Science Department, Rensselaer Polytechnic Institute, 110 8th St. Troy, NY 12180, USA. salems@cs.rpi.edu
authors.forename: Saeed
authors.initials: S
authors.lastname: Salem
authors.forename: Mohammed J
authors.initials: MJ
authors.lastname: Zaki
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid
chemical_list: D011506:Proteins