version 1.2 | 2006-09

Structural alignments for proteins with non-trivial relationships

Sisyphus: in greek: crafty

Authors:

Antonina Andreeva, Andreas Prlic, Tim Hubbard, Alexey Murzin sisyphus@mrc-lmb.cam.ac.uk

With the increasing amount of structural data, the number of homologous protein structures bearing topological irregularities is steadily growing. These include proteins with circular permutations, segment-swapping, context-dependent folding or chameleon sequences that can adopt alternative secondary structures [1]. Most of these non-trivial protein relationships are readily identified during the systematic analysis in our SCOP (Structural Classification of Proteins) database [2]. However, their automatic identification using the existing computational tools still remains difficult or impossible. Such non-trivial cases of protein relationships are known to pose a problem to the multiple alignment algorithms and to impede the comparative modeling studies. They support a new emerging concept of evolutionary changeable protein fold and thus create practical difficulties to the hierarchical protein structural classifications.

To facilitate the understanding and to provide a comprehensive annotation of proteins with such non-trivial structural relationships we have created SISYPHUS, a compendium to the SCOP database. The SISYPHUS database contains a collection of manually curated structural alignments and their interrelationships. Each multiple alignment within the SISYPHUS database consists of structurally similar regions common to a group of proteins. These regions range from oligomeric biological units, or individual domains to fragments of different size representing either internal structural repeats or motifs common to structurally distinct proteins. The SISYPHUS multiple alignments are displayed with SPICE, a browser that provides an integrated view of protein sequences, structures and their annotations [3].

References

1.Evolution of protein fold in the presence of functional constraints.
Andreeva A, Murzin A.G
Curr Opin Struct Biol. 2006 Jun;16(3):399-408
[pubmed] [pdf]
2. SCOP: a structural classification of proteins database for the investigation of sequences and structures.
Murzin A. G., Brenner S. E., Hubbard T., Chothia C.
J. Mol. Biol. 1995 247, 536-540.
[pubmed] [pdf]
3. Adding some SPICE to DAS
Prlic-A, Down-TA, Hubbard-TJP
Bioinformatics. 2005 Volume 21, suppl_2 Pp. ii40-ii41
[pubmed] [pdf]
The SISYPHUS alignments are grouped into three categories: please proceed to the categories page to learn more.

History

the SISYPHUS release history.