SISYPHUS—structural alignments for proteins with non-trivial relationships
By Antonina Andreeva, Andreas Prlic, Tim J. P. Hubbard, Alexey G. Murzin. 2006
82 citations recorded by the source corpus.
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. Their non-trivial structural relationships are readily identified during expert analysis but 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 multiple alignment algorithms and to impede comparative modeling studies. They support a new emerging concept of evolutionary changeable protein fold, which creates practical difficulties for the hierarchical classifications of protein structures.To facilitate the understanding of, and to provide a comprehensive annotation of proteins with such non-trivial structural relationships we have created SISYPHUS ([Σισυϕος]—in Greek crafty), a compendium to the SCOP database. The SISYPHUS database contains a collection of manually curated structural alignments and their inter-relationships. The multiple alignments are constructed for protein structural regions that range from oligomeric biological units, or individual domains to fragments of different size. The SISYPHUS multiple alignments are displayed with SPICE, a browser that provides an integrated view of protein sequences, structures and their annotations. The database is available from .
Subfields: Materials Chemistry, Molecular Biology
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Materials Chemistry
- John-Marc Chandonia
- Steven E. Brenner
- Kazutaka Katoh
- Alexey G. Murzin
- Antonina Andreeva
- Cyrus Chothia
- John Rozewicki
- Karlou Mar Amada
In Molecular Biology
- John-Marc Chandonia
- Steven E. Brenner
- Daron M. Standley
- Antonina Andreeva
- Kazutaka Katoh
- John Rozewicki
- Cyrus Chothia
- Alexey G. Murzin
Citations in the corpus
- Data growth and its impact on the SCOP database: new developments (2007, methodology): “Other complications for a hierarchical classification come from the discoveries of probable remote homologies between superfamilies of distinct protein folds and the non-trivial structural relationships within sequence families (8,9).”
- Pre-calculated protein structure alignments at the RCSB PDB website (2010, unknown): “We have recently improved CE to be able to detect circularly implementation is available as an option of the RCSB Protein Comparison / 221188 Tool. y s t APPROACH CE and FATCAT on”
- MAFFT-DASH: integrated protein sequence and structural alignment (2019, methodology): “In our benchmarks using 878 cases from the BAliBase, HomFam, OXFam, Mattbench and SISYPHUS datasets, MAFFT-DASH showed 10–20% improvement over standard MAFFT for MSA problems with weak similarity, in terms of Sum-of-Pairs (SP), a measure of how well a program succeeds at aligning input sequences in ”
- MUSTANG-MR Structural Sieving Server: Applications in Protein Structural Analysis and Crystallography (2010, methodology): “The ordinate gives the ‘Q score’ (or proportion of correctly aligned residue pairs) between SISYPHUS and ‘sieved’ alignments.”
- Advances and pitfalls of protein structural alignment. (2009, unknown): “The first two depend on a manually curated reference alignment (e.g. HOMSTRAD [45], CDD [46,47], Sisyphus [48], BIRC [49]), or classification (e.g. SCOP [50] and CATH [51]) as the standard of truth.”