CD-Search: protein domain annotations on the fly

By Aron Marchler-Bauer, Stephen H. Bryant. Nucleic Acids Res., 2004

2,096 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/cc613ac11087f032490cba8cae5621470932df68

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Citations in the corpus

Three Genomes from the Phylum Acidobacteria Provide Insight into the Lifestyles of These Microorganisms in Soils (2009, methodology): “These are subunits of the enterobactin synthase multienzyme complex (identified by SEARCHPKS [92] and CD-Search [54]).”
CDD/SPARCLE: the conserved domain database in 2020 (2019, methodology): “CD-Search displays not only domain and feature annotation, but also the name and functional characterization assigned to the corresponding SDA, if available via SPAR-CLE.”
CDD: a Conserved Domain Database for the functional annotation of proteins (2010, methodology): “The application that visualizes live or pre-computed search results has been termed CD-Search (7), and the underlying algorithm is Reverse Position-Specific BLAST (RPS-BLAST), a variation of the commonly used PSI-BLAST method (8,9).”
COBALT: constraint-based alignment tool for multiple protein sequences (2007, methodology): “Using the RPS-BLAST tool (the core search algorithm for the service described by Marchler-Bauer and Bryant (2004)), we can quickly search for domains in CDD that match to regions of input sequences.”
CDD: a conserved domain database for interactive domain family analysis (2006, neutral): “4) request (Figure 1a).”
CDD: conserved domains and protein three-dimensional structure (2012, methodology): “Figure 2 gives an example of a CD-Search graphical results summary obtained for a nucleotide query representing a complete viral genome.”
OrfPredictor: predicting protein-coding regions in EST-derived sequences (2005, methodology): “The predicted protein sequences can then be used as the input for additional annotation tools, such as InterProScan (5), for identifying protein families, domains and functional sites, the Conserved Domain Search service (6) for the detection of structural and functional domains, and SignalP (7) for”
Normal microRNA Maturation and Germ-Line Stem Cell Maintenance Requires Loquacious, a Double-Stranded RNA-Binding Domain Protein (2005, background): “To identify a dsRBD protein partner for Dcr-1, we searched the conserved domain database [37] for all Drosophila proteins that contain dsRBDs.”
CDD: specific functional annotation with the Conserved Domain Database (2008, methodology): “� Information about conserved sites, such as active sites and binding interfaces, is now displayed by CD-Search ( 6 ), the web service that visualizes domain annotation in CDD.”
CDD: NCBI's conserved domain database (2014, background): “01) for CDSearch (8) and CDD data production was not changed, as the overall coverage obtained with the CDD annotation resource was not affected by the change in scoring.”
CDD: a Conserved Domain Database for protein classification (2004, background): “Users of the CD-Search resource (4) may face multiple overlapping annotations, sometimes with very similar scores but distinct functional association.”
P2CS: a two-component system resource for prokaryotic signal transduction research (2009, methodology): “…a given gene, the software provides database links to investigate structural and functional domains of the corresponding protein sequence using the Conserved Domain Search service [22], the Simple Modular Architecture Research Tool [23] and the TMHMM transmembrane topology prediction method [24].”