Difference between revisions of "Superpose"
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| − | '''superpose''' - structural alignment based on secondary structure matching. It is part of the [[Ccp4|CCP4]] package and was written by Eugene Krissinel of the European Bioinformatics Institute, Cambridge, UK. | + | '''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|CCP4]] package and was written by Eugene Krissinel of the European Bioinformatics Institute, Cambridge, UK. |
==Background== | ==Background== | ||
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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). | 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 | Several approaches to protein structure alignment have been explored over the past decade. The techniques used | ||
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*depth-first recursive search on SSE (DEJAVU; Kleywegt & Jones, 1997); and | *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). | *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). | ||
| + | |||
| + | ==See also== | ||
| + | ===Web servers=== | ||
| + | *DALI | ||
| + | *VAST | ||
| + | *CE | ||
| + | *DEJAVU | ||
==References== | ==References== | ||
<references/> | <references/> | ||
| + | ===Further reading=== | ||
| + | *Rouvray et al., 1979, and references therein — addresses the problems of structure comparison and recognition by the graph-theoretical approach. | ||
==External links== | ==External links== | ||
| + | *[http://www.ebi.ac.uk/msd-srv/ssm Secondary Structure Matching (SSM) web server] | ||
*[http://www.ccp4.ac.uk/dist/html/superpose.html superpose - man page] | *[http://www.ccp4.ac.uk/dist/html/superpose.html superpose - man page] | ||
[[Category:Ccp4]] | [[Category:Ccp4]] | ||
Revision as of 23:04, 31 July 2007
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).
See also
Web servers
- DALI
- VAST
- CE
- DEJAVU
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.
