title: An initial strategy for comparing proteins at the domain architecture level.
abstract: BACKGROUND
  Ideally, only proteins that exhibit highly similar domain architectures should be compared with one another as homologues or be classified into a single family. By combining three different indices, the Jaccard index, the Goodman-Kruskal gamma function and the domain duplicate index, into a single similarity measure, we propose a method for comparing proteins based on their domain architectures.
  
  
  RESULTS
  Evaluation of the method using the eukaryotic orthologous groups of proteins (KOGs) database indicated that it allows the automatic and efficient comparison of multiple-domain proteins, which are usually refractory to classic approaches based on sequence similarity measures. As a case study, the PDZ and LRR_1 domains are used to demonstrate how proteins containing promiscuous domains can be clearly compared using our method. For the convenience of users, a web server was set up where three different query interfaces were implemented to compare different domain architectures or proteins with domain(s), and to identify the relationships among domain architectures within a given KOG from the Clusters of Orthologous Groups of Proteins database.
  
  
  CONCLUSIONS
  The approach we propose is suitable for estimating the similarity of domain architectures of proteins, especially those of multidomain proteins.
  
  
  BACKGROUND
  http://cmb.bnu.edu.cn/pdart/.
authors.affiliation: MOE Key Laboratory for Biodiversity Science and Ecological Engineering and College of Life Sciences, Beijing Normal University, Beijing 100875, China. linkui@bnu.edu.cn
authors.forename: Kui
authors.initials: K
authors.lastname: Lin
authors.forename: Lei
authors.initials: L
authors.lastname: Zhu
authors.forename: Da-Yong
authors.initials: DY
authors.lastname: Zhang
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000145:classification; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D011506:Proteins