title: Alignment algorithm for homology modeling and threading.
abstract: A DNA/protein sequence comparison is a popular computational tool for molecular biologists. Finding a good alignment implies an evolutionary and/or functional relationship between proteins or genomic loci. Sequential similarity between two proteins indicates their structural resemblance, providing a practical approach for structural modeling, when structure of one of these proteins is known. The first step in the homology modeling is a construction of an accurate sequence alignment. The commonly used alignment algorithms do not provide an adequate treatment of the structurally mismatched residues in locally dissimilar regions. We propose a simple modification of the existing alignment algorithm which treats these regions properly and demonstrate how this modification improves sequence alignments in real proteins.
authors.affiliation: Amgen, Inc., Thousand Oaks, California 91320-1789, USA. nicka@amgen.com
authors.forename: N N
authors.initials: NN
authors.lastname: Alexandrov
authors.forename: R
authors.initials: R
authors.lastname: Luethy
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D018257:Helix-Loop-Helix Motifs; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017386:Sequence Homology, Amino Acid