Conserved domain database

Aron Marchler-Bauer, Myra K.

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Conserved domain database

Conserved Domains and Protein Classification. HOW TO. Citing the Resources. The conserved domain database in Nucleic Acids Res. CD-Search: protein domain annotations on the fly. Epub Nov CDD: a conserved domain database for interactive domain family analysis. CDART: protein homology by domain architecture. Genome Res. Additional Journal Articles. Database resources of the National Center for Biotechnology Information. Database resources of the National Center for Biotechnology Information in InterPro in

Database Oxford. Myra K Derbyshire.

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.

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

A domain architecture is defined as the sequential order of conserved domains in a protein sequence. Regardless of which method you use, the results will display a list of similar domain architectures , which are ranked by the number of domains they share in common with the query protein's domain architecture. The results display also provides links to the proteins that have a each architecture. Click on any frame of the image below to link to corresponding sections in the CDART help document, which provide additional details about the input options and output display. Click on any frame of the image above to link to subsequent sections in this help document, which provide additional details about the input options and output display. Conserved Domains and Protein Classification. HOW TO. How to find proteins with similar domain architectures. Method 1: illustrated below.

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We continue to add novel domain family models to the collection and to establish hierarchical classifications of selected protein domain families where they will have a significant impact on protein naming by domain architecture. CDD: a conserved domain database for interactive domain family analysis. The SCOP database in expanded classification of representative family and superfamily domains of known protein structures. CDD is a protein annotation resource that consists of a collection of well-annotated multiple sequence alignment models for ancient domains and full-length proteins. More than 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 footprints. Open in new tab. Advance article alerts. Contents move to sidebar hide. CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Sillitoe I. Select Format Select format. Views 4, Add comment Cancel.

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You must accept the terms and conditions. Mingzhang Yang , Mingzhang Yang. CD-Search will then evaluate alternative domain architectures that can be formed including all the original hits and one or more of the additional domain hits. Revised 1 December The national center for biotechnology information's protein clusters database. Article Talk. Figure 1. CATH: increased structural coverage of functional space. Renata C. Identification of G-quadruplex-interacting proteins in living cells using an artificial G4-targeting biotin ligase. Individual residues that are parts of functional sites but not structural motifs are highlighted in bold font. Close mobile search navigation Article Navigation. Policy Name.