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

TLDR

NCBI’s Conserved Domain Database (CDD) annotates protein sequences with conserved domain footprints and functional sites, but its import of external domain family models makes it partially redundant. The study aims to simplify protein annotation by clustering redundant and homologous domain models into superfamilies. CDD uses manually curated, hierarchically organized domain models refined with 3D structure, clusters redundant and homologous families into superfamilies, and provides pre‑computed annotations and a Batch CD‑Search interface for large‑scale protein queries. Domain footprints are annotated with superfamily designations by default, with additional specific annotations indicating high‑confidence family membership. CDD is available at http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml.

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 .