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Aron Marchler-Bauer,
Chanjuan Zheng,
Farideh Chitsaz, Myra K Derbyshire,
Lewis Y Geer,
Renata C Geer,
Noreen R Gonzales,
Marc Gwadz,
David I Hurwitz,
Christopher J Lanczycki,
Fu Lu,
Shennan Lu,
Gabriele H Marchler,
James S Song,
Narmada Thanki,
Roxanne A Yamashita,
Dachuan Zhang,
Stephen H Bryant
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ABSTRACT: CDD, the Conserved Domain Database, is part of NCBI's Entrez query and retrieval system and is also accessible via http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml. CDD provides annotation of protein sequences with the location of conserved domain footprints and functional sites inferred from these footprints. Pre-computed annotation is available via Entrez, and interactive search services accept single protein or nucleotide queries, as well as batch submissions of protein query sequences, utilizing RPS-BLAST to rapidly identify putative matches. CDD incorporates several protein domain and full-length protein model collections, and maintains an active curation effort that aims at providing fine grained classifications for major and well-characterized protein domain families, as supported by available protein three-dimensional (3D) structure and the published literature. To this date, the majority of protein 3D structures are represented by models tracked by CDD, and CDD curators are characterizing novel families that emerge from protein structure determination efforts.
Nucleic Acids Research 11/2012; · 8.03 Impact Factor
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ABSTRACT: The overwhelming fraction of proteins whose sequences have been collected in comprehensive databases may never be assessed for function experimentally. Commonly, putative function is assigned based on similarity to experimentally characterized homologs, either on the level of the entire protein or for single evolutionarily conserved domains. The annotation of individual sites provides more detailed insights regarding the correspondence between sequence and function, as well as context for the interpretation of sequence variation and the outcomes of experiments. In general, site annotation has to be extracted from the published literature, and can often be transferred to closely related sequence neighbors. The National Center for Biotechnology Information's Conserved Domain Database (CDD) provides a system for curators to record functional (such as active sites or binding sites for cofactors) or characteristic sites (such as signature motifs), which are conserved across domain families, and for the transfer of that annotation to protein database sequences via high-confidence domain matches. Recently, CDD curators have begun to sort-site annotations into seven categories (active, polypeptide binding, nucleic acid binding, ion binding, chemical binding, post-translational modification and other) and here we present a first comparative analysis of sites obtained via domain model matches, juxtaposed with existing site annotation encountered in high-quality data sets. Site annotation derived from domain annotation has the potential to cover large fractions of protein sequences, and we observe that CDD-based site annotation complements existing site annotation in many cases, which may, in part, originate from CDD's curation practice of collecting sites conserved across diverse taxa and supported by evidence from multiple 3D structures.
Database The Journal of Biological Databases and Curation 01/2012; 2012:bar058. · 2.07 Impact Factor
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Aron Marchler-Bauer,
Shennan Lu,
John B Anderson,
Farideh Chitsaz, Myra K Derbyshire,
Carol DeWeese-Scott,
Jessica H Fong,
Lewis Y Geer,
Renata C Geer,
Noreen R Gonzales, [......],
Mikhail Mullokandov,
Marina V Omelchenko,
Cynthia L Robertson,
James S Song,
Narmada Thanki,
Roxanne A Yamashita,
Dachuan Zhang,
Naigong Zhang,
Chanjuan Zheng,
Stephen H Bryant
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[hide abstract]
ABSTRACT: NCBI's Conserved Domain Database (CDD) is a resource for the annotation of protein sequences with the location of conserved domain footprints, and functional sites inferred from these footprints. CDD includes manually curated domain models that make use of protein 3D structure to refine domain models and provide insights into sequence/structure/function relationships. Manually curated models are organized hierarchically if they describe domain families that are clearly related by common descent. As CDD also imports domain family models from a variety of external sources, it is a partially redundant collection. To simplify protein annotation, redundant models and models describing homologous families are clustered into superfamilies. By default, domain footprints are annotated with the corresponding superfamily designation, on top of which specific annotation may indicate high-confidence assignment of family membership. Pre-computed domain annotation is available for proteins in the Entrez/Protein dataset, and a novel interface, Batch CD-Search, allows the computation and download of annotation for large sets of protein queries. CDD can be accessed via http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml.
Nucleic Acids Research 01/2011; 39(Database issue):D225-9. · 8.03 Impact Factor
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Aron Marchler-Bauer,
John B Anderson,
Farideh Chitsaz, Myra K Derbyshire,
Carol DeWeese-Scott,
Jessica H Fong,
Lewis Y Geer,
Renata C Geer,
Noreen R Gonzales,
Marc Gwadz, [......],
Shennan Lu,
Gabriele H Marchler,
Mikhail Mullokandov,
James S Song,
Asba Tasneem,
Narmada Thanki,
Roxanne A Yamashita,
Dachuan Zhang,
Naigong Zhang,
Stephen H Bryant
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ABSTRACT: NCBI's Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution. The collection can be accessed at http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml, and is also part of NCBI's Entrez query and retrieval system, cross-linked to numerous other resources. CDD provides annotation of domain footprints and conserved functional sites on protein sequences. Precalculated domain annotation can be retrieved for protein sequences tracked in NCBI's Entrez system, and CDD's collection of models can be queried with novel protein sequences via the CD-Search service at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi. Starting with the latest version of CDD, v2.14, information from redundant and homologous domain models is summarized at a superfamily level, and domain annotation on proteins is flagged as either 'specific' (identifying molecular function with high confidence) or as 'non-specific' (identifying superfamily membership only).
Nucleic Acids Research 12/2008; 37(Database issue):D205-10. · 8.03 Impact Factor
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Aron Marchler-Bauer,
John B Anderson, Myra K Derbyshire,
Carol DeWeese-Scott,
Noreen R Gonzales,
Marc Gwadz,
Luning Hao,
Siqian He,
David I Hurwitz,
John D Jackson, [......],
Fu Lu,
Shennan Lu,
Gabriele H Marchler,
Mikhail Mullokandov,
James S Song,
Narmada Thanki,
Roxanne A Yamashita,
Jodie J Yin,
Dachuan Zhang,
Stephen H Bryant
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ABSTRACT: The conserved domain database (CDD) is part of NCBI's Entrez database system and serves as a primary resource for the annotation of conserved domain footprints on protein sequences in Entrez. Entrez's global query interface can be accessed at http://www.ncbi.nlm.nih.gov/Entrez and will search CDD and many other databases. Domain annotation for proteins in Entrez has been pre-computed and is readily available in the form of 'Conserved Domain' links. Novel protein sequences can be scanned against CDD using the CD-Search service; this service searches databases of CDD-derived profile models with protein sequence queries using BLAST heuristics, at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi. Protein query sequences submitted to NCBI's protein BLAST search service are scanned for conserved domain signatures by default. The CDD collection contains models imported from Pfam, SMART and COG, as well as domain models curated at NCBI. NCBI curated models are organized into hierarchies of domains related by common descent. Here we report on the status of the curation effort and present a novel helper application, CDTree, which enables users of the CDD resource to examine curated hierarchies. More importantly, CDD and CDTree used in concert, serve as a powerful tool in protein classification, as they allow users to analyze protein sequences in the context of domain family hierarchies.
Nucleic Acids Research 02/2007; 35(Database issue):D237-40. · 8.03 Impact Factor
