CDART: protein homology by domain architecture.

By Lewis Y. Geer, Michael Domrachev, David J. Lipman, Stephen H. Bryant. Genome Research, 2002

705 citations recorded by the source corpus.

The Conserved Domain Architecture Retrieval Tool (CDART) performs similarity searches of the NCBI Entrez Protein Database based on domain architecture, defined as the sequential order of conserved domains in proteins. The algorithm finds protein similarities across significant evolutionary distances using sensitive protein domain profiles rather than by direct sequence similarity. Proteins similar to a query protein are grouped and scored by architecture. Relying on domain profiles allows CDART to be fast, and, because it relies on annotated functional domains, informative. Domain profiles are derived from several collections of domain definitions that include functional annotation. Searches can be further refined by taxonomy and by selecting domains of interest. CDART is available at http://www.ncbi.nlm.nih.gov/Structure/lexington/lexington.cgi.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/080341acfee322645fbe24b97076009e0bd1b6d2

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In Molecular Biology

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Citations in the corpus

• The Hcp proteins fused with diverse extended-toxin domains represent a novel pattern of antibacterial effectors in type VI secretion systems (2017, methodology): “A bioinformatics screen for this specific domain-architecture was performed using the CDART tool as described previously.(55) Using these screened Hcp-ETs, BLASTP analyses were performed against the non-redundant protein database (ftp://ftp.”
• CDD: NCBI's conserved domain database (2014, methodology): “More than 700 individual domain model pairs were blocked from forming clusters as a result of this review, largely avoiding false clusters that would confound domain architecture analysis available via the CDART resource (9), as the latter depends on the assignment of superfamily-level domain footpr”
• CAZymes Analysis Toolkit (CAT): web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database. (2010, methodology): “Availability of the Pfam annotation and the protein sequences in the CAZy reference dataset creates an opportunity for researches to engage a number of sequence-based or Pfambased computational tools to study CAZymes, like PfamAlyzer (Hollich and Sonnhammer 2007), CDART (Geer et al. 2002), ArchSchem”
• CDD/SPARCLE: the conserved domain database in 2020 (2019, background): “ture Retrieval Tool) service (9) groups proteins in the Entrez database by common domain superfamily architecture.”
• CDD: specific functional annotation with the Conserved Domain Database (2008, methodology): “Starting with the development of the CDART resource (7), domain models in CDD have been clustered in order to deal with redundancy.”
• CDD: a curated Entrez database of conserved domain alignments (2003, background): “CDART, which stores that information, can be invoked from within Entrez to visualize domain architectures (6).”
• CDD/SPARCLE: functional classification of proteins via subfamily domain architectures (2016, methodology): “Since its inception, the facility of the Conserved Domain Database was enhanced by the CDART (Conserved Domain Architecture Retrieval Tool) service (9), which groups proteins in the Entrez database by common domain architecture.”
• CDD: a conserved domain database for interactive domain family analysis (2006, methodology): “Links to protein sequences reflect the results of pre-computed RPS–BLAST searches and are updated on a daily basis and stored in the CDART database (7).”
• Database resources of the National Center for Biotechnology Information: update (2004, background): “The Conserved Domain Architecture Retrieval Tool (CDART) (28) allows searches of protein databases on the basis of a conserved domain and returns the domain architectures of database proteins containing the query domain.”
• NCBI’s Conserved Domain Database and Tools for Protein Domain Analysis (2019, methodology): “An example Search for similar architecture (CDART; Geer et al., 2002) output for the myosin motor domain test set is shown in Figure 13.”
• CDD: conserved domains and protein three-dimensional structure (2012, background): “Architecture Retrieval Tool (CDART) service (15), which has been completely overhauled recently.”
• Nature of the protein universe (2009, methodology): “The NCBI provided us with the first deposit dates of NR sequences to February 7, 2009.”
• Structural basis for loading and inhibition of a bacterial T6SS phospholipase effector by the VgrG spike (2020, positive): “Protein domains were identified using Pfam (Sonnhammer et al , 1997) or CDart (Geer et al , 2002).”
• Outcome of a Workshop on Applications of Protein Models in Biomedical Research (2009, methodology): “The domains were defined based on the CDART resource at NCBI (Geer et al., 2002), which contains almost 30,000 domain families.”
• CDD: a Conserved Domain Database for protein classification (2004, methodology): “Pre-calculated CD-Searches for proteins are recorded in the CDART database (8), which provides summaries of domain architecture for all proteins in Entrez.”