The Conserved Domain Database (CDD) is a protein classification tool developed by the National Center for Biotechnology Information (NCBI). It is part of the Entrez query and retrieval system and is accessible via http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd. CD-Search, an interactive tool for identifying conserved domains in protein sequences, is available at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi. CDD is linked to other Entrez databases such as Proteins, Taxonomy, and PubMed. It provides links between proteins and domain models, and computational annotations can be viewed upon request. Protein-protein queries submitted to NCBI's BLAST search service are scanned for conserved domains by default. CDD started as a mirror of publicly available domain alignment collections, such as SMART, Pfam, and COG, but has since been updated and curated at NCBI. The goal is to create a more accurate and comprehensive database of conserved domain alignments. CDD includes domain models from Pfam, COG, SMART, and NCBI-curated models. The default CDD v2.01 retains only a subset of these models due to redundancy and lineage-specificity. CDD provides access to pre-calculated CD-Search results for proteins in Entrez, which include domain architecture summaries. The database is accessible through the Entrez data retrieval system and can be queried as the 'Domains' database. CDD also includes position-specific scoring matrices for use with RPS-BLAST. CDD is used to identify conserved domains in protein sequences, and the results are displayed graphically. The database includes information on conserved features such as active sites and binding interfaces. Users can access additional annotations, such as links to literature and textbooks. CDD is a major resource for protein classification and domain annotation. It is used to build domain family hierarchies and record conserved features. The database is continuously updated and maintained, and future developments include distributing software for building and maintaining these hierarchies. CDD is an essential tool for researchers in the field of bioinformatics and molecular biology.The Conserved Domain Database (CDD) is a protein classification tool developed by the National Center for Biotechnology Information (NCBI). It is part of the Entrez query and retrieval system and is accessible via http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd. CD-Search, an interactive tool for identifying conserved domains in protein sequences, is available at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi. CDD is linked to other Entrez databases such as Proteins, Taxonomy, and PubMed. It provides links between proteins and domain models, and computational annotations can be viewed upon request. Protein-protein queries submitted to NCBI's BLAST search service are scanned for conserved domains by default. CDD started as a mirror of publicly available domain alignment collections, such as SMART, Pfam, and COG, but has since been updated and curated at NCBI. The goal is to create a more accurate and comprehensive database of conserved domain alignments. CDD includes domain models from Pfam, COG, SMART, and NCBI-curated models. The default CDD v2.01 retains only a subset of these models due to redundancy and lineage-specificity. CDD provides access to pre-calculated CD-Search results for proteins in Entrez, which include domain architecture summaries. The database is accessible through the Entrez data retrieval system and can be queried as the 'Domains' database. CDD also includes position-specific scoring matrices for use with RPS-BLAST. CDD is used to identify conserved domains in protein sequences, and the results are displayed graphically. The database includes information on conserved features such as active sites and binding interfaces. Users can access additional annotations, such as links to literature and textbooks. CDD is a major resource for protein classification and domain annotation. It is used to build domain family hierarchies and record conserved features. The database is continuously updated and maintained, and future developments include distributing software for building and maintaining these hierarchies. CDD is an essential tool for researchers in the field of bioinformatics and molecular biology.