Abstract
BackgroundProtein 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.MethodsHere 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.ResultsThe mapping results show a general agreement between the two databases, as well as many interesting areas of disagreement. In the cases of disagreement, the functional and evolutionary characteristics of the domains are examined to determine which domain definition is biologically more informative.
Highlights
Protein domains have long been an ill-defined concept in biology
Materials All Protein Data Bank (PDB) protein sequences, based on PDB SEQRES records, with less than 95% identity to each other were downloaded from the ASTRAL Compendium [18,19]
Domain mapping A total of 2081 Pfam families and 2512 SCOP domain families are defined in the set of 8259 PDB protein chains
Summary
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. Protein domains are generally considered as protein fragments of common structures which may independently fold [4] or have their own functions [5]. They have been treated as evolutionary units [6]. Classifying proteins based on their constituent domains is one of the most effective and efficient approaches to organize protein data both by structures and by evolutionary relationships. The challenge lies in the ambiguity of domain definitions, as well as the lack of useful structural information about most proteins
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