Conserved domain database

The Conserved Domain Database CDD is a database of well-annotated multiple sequence alignment models and derived database search models, conserved domain database, for ancient domains and full-length proteins. These two classifications coincide rather often, as a matter of fact, and what is found as an independently folding unit of a polypeptide chain also carries specific function.

Conserved Domains and Protein Classification. HOW TO. Citing the Resources. The conserved domain database in Nucleic Acids Res.

Conserved domain database

Aron Marchler-Bauer, Myra K. Derbyshire, Noreen R. Geer, Renata C. Hurwitz, Christopher J. Lanczycki, Fu Lu, Gabriele H. Marchler, James S. Going forward, we strive to improve the coverage and consistency of domain annotation provided by CDD. We maintain a live search system as well as an archive of pre-computed domain annotation for sequences tracked in NCBI's Entrez protein database, which can be retrieved for single sequences or in bulk. We also maintain import procedures so that CDD contains domain models and domain definitions provided by several collections available in the public domain, as well as those produced by an in-house curation effort. The curation effort aims at increasing coverage and providing finer-grained classifications of common protein domains, for which a wealth of functional and structural data has become available. CDD curation generates alignment models of representative sequence fragments, which are in agreement with domain boundaries as observed in protein 3D structure, and which model the structurally conserved cores of domain families as well as annotate conserved features. The amount of sequence data deposited into public repositories has made it impracticable to routinely run sequence similarity searches against single, generic and comprehensive sequence collections. A search set that grows exponentially in size does not fit well with the need for executing an ever increasing number of such searches—and quicker searches too, if possible. Curated collections of representative sequences offer a viable alternative, and so do profile database searches, as collections of profile models that represent evolutionarily conserved sequence fragments or domains are not expected to grow at an exorbitant pace.

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CDD has been available publicly for over 20 years and has grown substantially during that time. Maintaining an archive of pre-computed annotation continues to be a challenge and has slowed down the cadence of CDD releases. CDD aims to collect a comprehensive set of protein and domain family models, and it does allow for considerable redundancy in the model set, to ensure good coverage of the protein space. Models that provide significantly overlapping annotation are clustered into protein domain superfamilies, and when domain annotation fails to exceed critical model-specific score thresholds, CDD by default reports superfamily annotation rather than individual model hits. For each model, we compute a consensus sequence, which is used for display purposes only, and reflects the length of the position-specific score matrix PSSM. While consensus sequences are visible and made available, CDD is not a sequence collection, but is rather meant to enrich the annotation of existing sequence collections. The current CDD version, v3.

Protein or Nucleotide Query Sequence. Batch of Protein Sequences. Find proteins with similar domain architectures. Conserved Domains and Protein Classification. HOW TO. Search Methods: Quick Start Guide. Text Term Search. Retrieve conserved domain records that contain a term s of interest e.

Conserved domain database

Identify the putative function of a protein sequence. Identify a protein's classification based on domain architecture. Identify the amino acids in a protein sequence that are putatively involved in functions such as binding or catalysis, as mapped from conserved domain annotations to the query sequence. View a query protein sequence embedded within the multiple sequence alignment of a domain model. Interactively view the 3D structure of a conserved domain. Find other proteins with similar domain architecture. Interactively view the phylogenetic sequence tree for a conserved domain model of interest with or without a query sequence embedded. Conserved Domains and Protein Classification. HOW TO.

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Mistry J. Science and Mathematics. Lanczycki, Fu Lu, Gabriele H. Jiyao Wang , Jiyao Wang. New issue alert. National Center for Biotechnology Information. Open in new tab Download slide. Gene Ontology Consortium. More metrics information. Marchler, James S. Type of access to data. H , DiCuccio M. Here, we briefly summarize recent updates to the CDD resource, with respect to its content and the functionality of search interfaces. Cytoscape: a software environment for integrated models of biomolecular interaction networks.

This page provides quick start guides for some common types of searches.

Initially, a uniform word-score threshold was used across the entire search database. HOW TO. Individual residues that are parts of functional sites but not structural motifs are highlighted in bold font. Models that provide significantly overlapping annotation are clustered into protein domain superfamilies, and when domain annotation fails to exceed critical model-specific score thresholds, CDD by default reports superfamily annotation rather than individual model hits. The upcoming CDD release v3. The conserved domain database in Please consider expanding the lead to provide an accessible overview of all important aspects of the article. United States. They also provide functional characterization that is based on the presence of signature sequence patterns and may serve as a starting point for functional annotation and classification. RefSeq: expanding the prokaryotic genome annotation pipeline reach with protein family model curation. Additional name s.