Generation of a consensus protein domain dictionary.
BACKGROUND
The discovery of new protein folds is a relatively rare occurrence even as the rate of protein structure determination increases. This rarity reinforces the concept of folds as reusable units of structure and function shared by diverse proteins. If the folding mechanism of proteins is largely determined by their topology, then the folding pathways of members of existing folds could encompass the full set used by globular protein domains.


RESULTS
We have used recent versions of three common protein domain dictionaries (SCOP, CATH and Dali) to generate a consensus domain dictionary (CDD). Surprisingly, 40% of the metafolds in the CDD are not composed of autonomous structural domains, i.e. they are not plausible independent folding units. This finding has serious ramifications for bioinformatics studies mining these domain dictionaries for globular protein properties. However, our main purpose in deriving this CDD was to generate an updated CDD to choose targets for MD simulation as part of our dynameomics effort, which aims to simulate the native and unfolding pathways of representatives of all globular protein consensus folds (metafolds). Consequently, we also compiled a list of representative protein targets of each metafold in the CDD.


METHODS
This domain dictionary is available at www.dynameomics.org.
Biomolecular Structure and Design Program, University of Washington, Seattle, WA 98195-5013, USA.
R Dustin
RD
Schaeffer
Amanda L
AL
Jonsson
Andrew M
AM
Simms
Valerie
V
Daggett
D019295:Computational Biology; D004014:Dictionaries as Topic; D008958:Models, Molecular; D058977:Molecular Sequence Annotation; D017510:Protein Folding; D017434:Protein Structure, Tertiary