|
CHOP is a method of dissecting proteins into domain-like fragments based on sequence homology. It is developed by Jinfeng Liu at the Rost Group, at Columbia University, New York.
Sequence-based domain assignment is one of the most important and challenging problems in structural biology. Many methods have been developed based on biochemical properties, statistics, sequence homology, and other aspects of predicted protein structure. Here, we present CHOP, a publicly available service for chopping proteins into fragments that resemble structural domains. Upon user submission of a protein sequence, CHOP will analyse the protein for its homology to PDB domains, Pfam domains and SWISS-PROT proteins. It will then return e-mail to the user about the putative domain assignments.
CHOP can be useful for biologists in several ways. For example, structural biologists can check the putative domain organization of the protein and make the decision about how to make proper constructs. Biologists interested in protein structure-function relationship may also find it interesting to pinpoint the structural domain that is particularly relevant to a specific function.
From this site you can:
If you find CHOP useful for your research, please cite:
-
Liu J & Rost B (2004) CHOP proteins into structural domain-like fragments. Proteins, 55(3):678-688 MEDLINE Paper text
-
Liu J & Rost B (2004) CHOP: Domain Dissection Based on Homology Nucleic Acids Research 32(Web Server issue):W569-71
|
