CDD: a Conserved Domain Database for the functional annotation of proteins

CDD: a Conserved Domain Database for the functional annotation of proteins

2010 | 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, Marc Gwadz, David I. Hurwitz, John D. Jackson, Zhaoxi Ke, Christopher J. Lanczycki, Fu Lu, Gabriele H. Marchler, Mikhail Mullokandov, Marina V. Omelchenko, Cynthia L. Robertson, James S. Song, Narmada Thanki, Roxanne A. Yamashita, Dachuan Zhang, Naigong Zhang, Chanjuan Zheng and Stephen H. Bryant
The Conserved Domain Database (CDD) is a resource for annotating protein sequences with the location of conserved domain footprints and inferred functional sites. CDD includes manually curated domain models that utilize protein 3D structure to refine domain models and provide insights into sequence-structure-function relationships. These models are organized hierarchically, reflecting common descent among related families. CDD also imports domain family models from external sources, making it a partially redundant collection. To simplify protein annotation, redundant models and homologous families are clustered into superfamilies. Pre-computed domain annotations are available for proteins in the Entrez/Protein dataset, and a novel interface, Batch CD-Search, allows for the computation and download of annotations for large sets of protein queries. CDD is updated several times a year and can be accessed via the NCBI website. The database supports cross-referencing with other databases such as Entrez Protein, PubMed, and NCBI BioSystems. CDD provides detailed information on specific hits, superfamily annotations, and multi-domain models, along with functional site annotations. The Batch CD-Search tool facilitates the processing of up to 100,000 protein queries, allowing users to download results in various formats.The Conserved Domain Database (CDD) is a resource for annotating protein sequences with the location of conserved domain footprints and inferred functional sites. CDD includes manually curated domain models that utilize protein 3D structure to refine domain models and provide insights into sequence-structure-function relationships. These models are organized hierarchically, reflecting common descent among related families. CDD also imports domain family models from external sources, making it a partially redundant collection. To simplify protein annotation, redundant models and homologous families are clustered into superfamilies. Pre-computed domain annotations are available for proteins in the Entrez/Protein dataset, and a novel interface, Batch CD-Search, allows for the computation and download of annotations for large sets of protein queries. CDD is updated several times a year and can be accessed via the NCBI website. The database supports cross-referencing with other databases such as Entrez Protein, PubMed, and NCBI BioSystems. CDD provides detailed information on specific hits, superfamily annotations, and multi-domain models, along with functional site annotations. The Batch CD-Search tool facilitates the processing of up to 100,000 protein queries, allowing users to download results in various formats.
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