Comparative mapping of sequence-based and structure-based protein domains.

ABSTRACT:

Background

Protein domains have long been an ill-defined concept in biology. They are generally described as autonomous folding units with evolutionary and functional independence. Both structure-based and sequence-based domain definitions have been widely used. But whether these types of models alone can capture all essential features of domains is still an open question.

Methods

Here we provide insight on domain definitions through comparative mapping of two domain classification databases, one sequence-based (Pfam) and the other structure-based (SCOP). A mapping score is defined to indicate the significance of the mapping, and the properties of the mapping matrices are studied.

Results

The mapping results show a general agreement between the two databases, as well

SUBMITTER: Zhang Y 

PROVIDER: S-EPMC1087832 | biostudies-literature | 2005 Mar

REPOSITORIES: biostudies-literature