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Updated: Jun 6, 2026
09:37
An Integrated Approach for Microprotein Identification and Sequence Analysis
Published on: July 12, 2022
CDD: a Conserved Domain Database for the functional annotation of proteins
Aron Marchler-Bauer1, Shennan Lu, John B Anderson
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA. bauer@ncbi.nlm.nih.gov
Nucleic Acids Research
|November 27, 2010
Summary
The Conserved Domain Database (CDD) annotates protein sequences with functional sites using curated models and 3D structures. It simplifies protein analysis by clustering domains into superfamilies for efficient annotation.
Area of Science:
- Bioinformatics
- Structural Biology
- Computational Biology
Background:
- Protein sequence annotation is crucial for understanding biological function.
- Conserved Domain Database (CDD) at NCBI provides annotations for protein sequences.
- Existing methods require efficient ways to manage and utilize domain information.
Purpose of the Study:
- To describe the NCBI's Conserved Domain Database (CDD) resource.
- To highlight CDD's capabilities in annotating protein sequences with conserved domain footprints and functional sites.
- To introduce the Batch CD-Search tool for large-scale annotation.
Main Methods:
- Utilizes manually curated domain models incorporating protein 3D structure.
- Hierarchically organizes related domain families.
- Clusters redundant and homologous models into superfamilies for simplified annotation.
Main Results:
- CDD provides accurate protein annotation by integrating sequence, structure, and function information.
- Superfamily clustering simplifies the assignment of domain footprints.
- Batch CD-Search enables efficient, large-scale annotation of protein datasets.
Conclusions:
- The Conserved Domain Database is a valuable resource for protein sequence annotation.
- Integration of 3D structure refines domain models and enhances functional inference.
- CDD and its Batch CD-Search tool streamline protein analysis workflows.
Related Concept Videos
01:49Conserved Binding Sites
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
01:49Conserved Binding Sites
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
02:26Conservation of Protein Domains
Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
02:26Conservation of Protein Domains Over Different Proteins
Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
03:36Genome Annotation and Assembly
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
02:51Multi-species Conserved Sequences
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...