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. 2004 Jul 1;32(Web Server issue):W569-71.
doi: 10.1093/nar/gkh481.

CHOP: parsing proteins into structural domains

Jinfeng Liu  1 , Burkhard Rost
Affiliations

CHOP: parsing proteins into structural domains

Jinfeng Liu et al. Nucleic Acids Res. .

Abstract

Sequence-based domain assignment is one of the most important and challenging problems in structural biology. We have developed a method, CHOP, that chops proteins into domain-like fragments. The basic idea is to cut proteins from entirely sequenced organisms beginning from very reliable experimental information (Protein Data Bank), proceeding to expert annotations of domain-like regions (Pfam-A) and completing through cuts based on termini of native protein ends. The CHOP server takes protein sequences as input and returns the dissections supported by homology transfer. CHOP results are precompiled for many entirely sequenced proteomes. The service is available at http://www.rostlab.org/services/CHOP/.

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Figures

Figure 1
Figure 1
Percentage of proteins chopped in 62 entire proteomes. (A) About two-thirds of the proteins from 62 proteomes can be chopped (absolute number of proteins in bars). (B) For the subset of proteins that can be chopped, about 30% of the prokaryotic and archaean proteins contain only one fragment that is homologous to either PrISM domains or Pfam-A fragments; this single domain fraction is considerably lower for eukaryotic proteins. Bars indicate the standard deviation of the distribution for these numbers over all three kingdoms.
See this image and copyright information in PMC

References

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