title: Using iterative dynamic programming to obtain accurate pairwise and multiple alignments of protein structures.
abstract: We show how a basic pairwise alignment procedure can be improved to more accurately align conserved structural regions, by using variable, position-dependent gap penalties that depend on secondary structure and by taking the consensus of a number of suboptimal alignments. These improvements, which are novel for structural alignment, are direct analogs of what is possible with normal sequences alignment. They are feasible for us since our basic structural alignment procedure, unlike others, is so similar to normal sequence alignment. We further present preliminary results that show how our procedure can be generalized to produce a multiple alignment of a family of structures. Our approach is based on finding a "median" structure from doing all possible pairwise alignments and then aligning everything to it.
authors.affiliation: Department of Structural Biology, Stanford University CA 94305, USA. mbg@hyper.stanford.edu
authors.forename: M
authors.initials: M
authors.lastname: Gerstein
authors.forename: M
authors.initials: M
authors.lastname: Levitt
mesh_terms: D000595:Amino Acid Sequence; D005914:Globins / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D016415:Sequence Alignment; D013762:Tetrahydrofolate Dehydrogenase / Q000737:chemistry
chemical_list: D005914:Globins; D013762:Tetrahydrofolate Dehydrogenase