Superpose
superpose - structural alignment based on secondary structure matching and is based on the Secondary Structure Matching (SSM) advanced graph-matching algorithm. It is part of the CCP4 package and was written by Eugene Krissinel of the European Bioinformatics Institute, Cambridge, UK.
Contents
[hide]Background
"While high sequence similarity almost always implies structural similarity, the opposite is not true. It is therefore expected that three-dimensional alignment will provide more significant clues to protein function and properties than sequence alignment alone".[1]
Most similarity measures are based on the evaluation of the size of common substructures, for example the length of alignment (the longer, the better), and a measure of the distance between them, such as r.m.s.d. (the lower, the better).
The graph-theoretical approach typically includes three major steps:
- graph representation of the objects in question;
- matching the graphs representing the objects; and
- evaluating the common subgraphs found in order to form conclusions about similarity.
Several approaches to protein structure alignment have been explored over the past decade. The techniques used include:
- comparison of distance matrices (DALI; Holm & Sander, 1993);
- analysis of differences in vector distance plots (Orengo & Taylor, 1996);
- minimization of the soap-bubble surface area between two protein backbones (Falicov & Cohen, 1996);
- dynamic programming on pairwise distances between the proteins' residues (Subbiah et al., 1993; Gerstein & Levitt, 1996, 1998);
- secondary-structure elements (SSEs) (Singh & Brutlag, 1997);
- three-dimensional clustering (Vriend & Sander, 1991; Mizuguchi & Go, 1995);
- graph theory (Mitchell et al., 1990; Alexandrov, 1996; Grindley et al., 1993);
- combinatorial extension of alignment path (CE; Shindyalov & Bourne, 1998);
- vector alignment of SSEs (VAST; Gibrat et al., 1996);
- depth-first recursive search on SSE (DEJAVU; Kleywegt & Jones, 1997); and
- many others (Zuker & Somorjai, 1989; Taylor & Orengo, 1989; Godzik & Skolnick, 1994; Russell & Barton, 1992; Sali & Blundell, 1990; Barakat & Dean, 1991; Leluk et al., 2003; Jung & Lee, 2000; Kato & Takahashi, 2001).
Most details of protein fold may be expressed in terms of just two types of SSEs, namely helices (including what type of helix) and strands.
Keywords
secondary-structure elements (SSEs)
See also
Web servers
- DALI
- VAST
- CE
- DEJAVU
Related
- PROMOTIF algorithm (Hutchinson & Thornton, 1996) — aids in calculating SSEs
References
- Jump up ↑ Krissinel E, Henrick K (2004). "Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions". Acta Cryst, D60:2256-2268.
Further reading
- Rouvray et al., 1979, and references therein — addresses the problems of structure comparison and recognition by the graph-theoretical approach.
