CD-Search: protein domain annotations on the fly

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W327-31. doi: 10.1093/nar/gkh454.


We describe the Conserved Domain Search service (CD-Search), a web-based tool for the detection of structural and functional domains in protein sequences. CD-Search uses BLAST(R) heuristics to provide a fast, interactive service, and searches a comprehensive collection of domain models. Search results are displayed as domain architecture cartoons and pairwise alignments between the query and domain-model consensus sequences. Search results may be visualized in further detail by embedding the query sequence into multiple alignment displays and by mapping onto three-dimensional molecular graphic displays of known structures within the domain family. CD-Search can be accessed at

MeSH terms

  • Amino Acid Sequence
  • Computer Graphics
  • Consensus Sequence
  • Internet
  • Protein Structure, Tertiary*
  • Proteins / chemistry
  • Sequence Alignment
  • Sequence Analysis, Protein*
  • Software*
  • Time Factors
  • User-Computer Interface


  • Proteins