课件 文献 资料Using Iterative Dynamic Programming to Obtain Accurate Pairwise and Multiple Alignments of Protein Structures.pdfVIP

Using Iterative Dynamic Programming to Obtain Accurate Pairwise and Multiple Alignments of Protein Structures Mark Gerstein Michael Levitt Department of Structural Biology, Fairchild D109 Stanford University, Stanford, CA 94305 { mbg,levitt} @ Abstract A number of procedures for automatic structural We show how a basic pa1rw1se alignment procedure alignment and comparison have been developed (Taylor can be improved to more accurately align conserved Orengo, 1989; Russell Barton, 1993; Holm Sander, struct ural regions, by using variable, position­ 1993; Sali Blundell, 1990; Godzik Skolnick, 1994; dependent gap penalties that depend on secondary Artymiuk et al., 1989; Subbiah et al., 1993; Laurents et al., stn比ture and by taking the consensus of a number of 1994). These procedures for structural alignment have suboptimal alignments. These improvements, which detected many interesting similarities in protein structure are novel for structural alignment, are direct analogs - e.g. the globin-colicin similarity (Holm Sander, of what is possible with normal sequence alignment. 1993b) and have been used to cluster the whole structure They are feasible for us since our basic structural databank on the basis of structural similarity (Holm alignme