CDD: a Conserved Domain Database for protein classification
Open accessAbstract
The Conserved Domain Database (CDD) is the protein classification component of NCBI's Entrez query and retrieval system. CDD is linked to other Entrez databases such as Proteins, Taxonomy and PubMed, and can be accessed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd. CD-Search, which is available at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi, is a fast, interactive tool to identify conserved domains in new protein sequences. CD-Search results for protein sequences in Entrez are pre-computed to provide links between proteins and domain models, and computational annotation visible upon request. Protein-protein queries submitted to NCBI's BLAST search service at http://www.ncbi.nlm.nih.gov/BLAST are scanned for the presence of conserved domains by default. While CDD started out as essentially a mirror of publicly available domain alignment collections, such as SMART, Pfam and COG, we have continued an effort to update, and in some cases replace these models with domain hierarchies curated at the NCBI. Here, we report on the progress of the curation effort and associated improvements in the functionality of the CDD information retrieval system.
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The conformation of Als1 is similar to that of the pfam02368 family of bacterial immunoglobulin-like domain surface protein/adhesins, which includes the invasin of Y. pseudotuberculosis.
“The conformation of Als1 is similar to that of the pfam02368 family of bacterial immunoglobulin-like domain surface protein/adhesins, which includes the invasin of Y. pseudotuberculosis [42,43].”
From Als3 Is a Candida albicans Invasin That Binds to Cadherins and Induces Endocytosis by Host Cells (2007) · cites this paper as [42]
The Introduction discusses domain families and structural comparisons generally, but does not address Als1 or the claimed resemblance. Searches for pfam02368, invasin, and bacterial immunoglobulin-like adhesins found no passage in our copy establishing the comparison or the family's membership. (LLM, conf=0.76)
Experimental — accuracy not yet measuredThe cleft motif of Als3 is more similar to that of the COG4886 family of leucine-rich repeat invasins/intimins.
“In contrast, the cleft motif of Als3 is more similar to that of the COG4886 family of leucine-rich repeat invasins/intimins [42].”
From Als3 Is a Candida albicans Invasin That Binds to Cadherins and Induces Endocytosis by Host Cells (2007) · cites this paper as [42]
The Introduction and Finding Domains in Entrez sections describe CDD and how it assesses domain-family similarity, but do not compare the Als3 cleft motif with any family. Searches for Als3, COG4886, and leucine-rich repeat invasins/intimins found no passage addressing the claimed resemblance. Page numbers were not available in our copy. (LLM, conf=0.76)
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- Authors
- Marchler-Bauer, A.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2004-12-17
- Volume
- 33
- Issue
- Database issue
- Pages
- D192-D196
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC540023
- OpenAlex
- W2133666768
- Cited by
- 1,156
- References
- 0
- Citations by year
- 2026: 4 · 2025: 14 · 2024: 15 · 2023: 21 · 2022: 26 · 2021: 23 · 2020: 10 · 2019: 17 · 2018: 23 · 2017: 18 · 2016: 33 · 2015: 33 · 2014: 41 · 2013: 41 · 2012: 43
- FWCI
- 52.57
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- other-oa
- Locations
- Nucleic Acids Research (publishedVersion, other-oa)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- protein domain annotation, conserved domains, protein classification, domain model, domain hierarchy, database curation, Entrez, BLAST, SMART, Pfam, COG
- MeSH terms
- Amino Acid Sequence, Phylogeny, Proteins, User-Computer Interface, Sequence Alignment, Conserved Sequence, Protein Structure, Tertiary, Sequence Analysis, Protein, Databases, Protein
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