title: Toward consistent assignment of structural domains in proteins.
abstract: The assignment of protein domains from three-dimensional structure is critically important in understanding protein evolution and function, yet little quality assurance has been performed. Here, the differences in the assignment of structural domains are evaluated using six common assignment methods. Three human expert methods (AUTHORS (authors' annotation), CATH and SCOP) and three fully automated methods (DALI, DomainParser and PDP) are investigated by analysis of individual methods against the author's assignment as well as analysis based on the consensus among groups of methods (only expert, only automatic, combined). The results demonstrate that caution is recommended in using current domain assignments, and indicates where additional work is needed. Specifically, the major factors responsible for conflicting domain assignments between methods, both experts and automatic, are: (1) the definition of very small domains; (2) splitting secondary structures between domains; (3) the size and number of discontinuous domains; (4) closely packed or convoluted domain-domain interfaces; (5) structures with large and complex architectures; and (6) the level of significance placed upon structural, functional and evolutionary concepts in considering structural domain definitions. A web-based resource that focuses on the results of benchmarking and the analysis of domain assignments is available at
authors.affiliation: San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0537, USA. veretnik@sd.sc.edu
authors.forename: Stella
authors.initials: S
authors.lastname: Veretnik
authors.forename: Philip E
authors.initials: PE
authors.lastname: Bourne
authors.forename: Nickolai N
authors.initials: NN
authors.lastname: Alexandrov
authors.forename: Ilya N
authors.initials: IN
authors.lastname: Shindyalov
mesh_terms: D000465:Algorithms; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins