CDD: a database of conserved domain alignments with links to domain three-dimensional structure

By Aron Marchler-Bauer, Anna R. Panchenko, Benjamin A. Shoemaker, Paul A. Thiessen, Lewis Y. Geer, Stephen H. Bryant. Nucleic Acids Res., 2002

672 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/32e9ad5353ea18904447116bf613e896adb9af25

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Citations in the corpus

The integrated microbial genomes (IMG) system (2005, methodology): “Genes are assigned to COGs based on RPS-BLAST (reverse position specific BLAST) and NCBI’s Conserved Domain Database (CDD) (10), with an E-value of 10 (2).”
The Biomolecular Interaction Network Database and related tools 2005 update (2004, background): “One can further speciﬁcally limit the complexity of the returned data to a backbone-only model (e.g. choose ‘virtual bond model’ before launching Cn3D) to improve the responsiveness of systems with insufﬁcient memory to display such large structures.”
BIND: the Biomolecular Interaction Network Database (2003, methodology): “The domain annotation is from SeqHound which contains a complete RPS-BLAST analysis of the GenBank or dataset, using the Conserved Domain Database (15) performed on our 216 Beowulf cluster.”
A hitchhiker's guide to expressed sequence tag (EST) analysis (2006, methodology): “In addition, one can scan for protein domains by selecting the (CDD) Conserved Domain Database [52] and the COG (Cluster of Orthologous Groups) [53] database using RPS-BLAST (Reverse PSI-BLAST) [52].”
Unique and Conserved Features of Genome and Proteome of SARS-coronavirus, an Early Split-off From the Coronavirus Group 2 Lineage (2003, methodology): “Genpeptides, Conserved domain (CD) 63 and protein family (Pfam) 64 databases were used in this study.”
Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners (2007, methodology): “Most methods begin by annotating protein sequences with domains that can be defined by Pfam, SCOP, CDD, or other domain databases [63–65].”
CDD: a curated Entrez database of conserved domain alignments (2003, methodology): “We have continued to mirror two public collections of conserved domain models, Pfam (1) and SMART (2), and to convert their alignment models into searchable databases of Position Specific Score Matrices (PSSMs) (3).”
Discovery and functional characterization of diverse Class 2 CRISPR-Cas systems (2015, methodology): “, 2015) using the RPS-BLAST program (Marchler-Bauer et al., 2002).”
NRPS-PKS: a knowledge-based resource for analysis of NRPS/PKS megasynthases (2004, methodology): “It may be noted that profile-based domain identification tools such as CDD (11) and InterPro (12) fail to identify the correct domain boundaries of C domains.”
CDD: a Conserved Domain Database for protein classification (2004, methodology): “Searchmodels for use with local RPS-BLAST installations, as well as CDD alignments are available at ftp://ftp.ncbi.nlm. nih.gov/pub/mmdb/cdd/.”
The HHpred interactive server for protein homology detection and structure prediction (2005, background): “Databases: A wide range of regularly updated structure and protein family databases can be searched: the PDB (21), SCOP (22), Pfam (23), SMART (24), COG (25) and CDD (26).”
PATRIC: the Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic Species (2011, methodology): “S4B), the set of protein sequences (total (cid:1) 2,771,151) encoded within 800 bacterial genomes (794 species) was used in RPSBLAST searches against the data set constructed in the ﬁrst step, with the identical search strategy and signiﬁcance threshold.”