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Related Concept Videos

Conservation of Protein Domains02:26

Conservation 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...
Conservation of Protein Domains Over Different Proteins02:26

Conservation 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...
Conserved Binding Sites01:49

Conserved 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...
Conserved Binding Sites01:49

Conserved 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...
Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...
Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...

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Mapping Dysfunctional Protein-Protein Interactions in Disease
09:39

Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

CDD: a conserved domain database for interactive domain family analysis.

Aron Marchler-Bauer1, John B Anderson, Myra K Derbyshire

  • 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Building 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA. bauer@ncbi.nlm.nih.gov

Nucleic Acids Research
|December 1, 2006
PubMed
Summary

The Conserved Domain Database (CDD) annotates protein sequences in Entrez. A new tool, CDTree, aids in protein classification by analyzing domain family hierarchies.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • The Conserved Domain Database (CDD) is a key resource within NCBI's Entrez system.
  • It provides pre-computed annotations of conserved domain footprints on protein sequences.
  • CDD integrates models from Pfam, SMART, and COG, alongside NCBI-curated domains.

Purpose of the Study:

  • To report on the status of CDD's curation efforts.
  • To introduce CDTree, a novel application for examining curated domain hierarchies.
  • To enhance protein classification through the combined use of CDD and CDTree.

Main Methods:

  • Utilizing Entrez's global query interface for database searches.
  • Employing the CD-Search service for scanning novel protein sequences against CDD-derived models via BLAST heuristics.
  • Leveraging CDTree to visualize and analyze hierarchical relationships among curated domains.

Main Results:

  • Pre-computed conserved domain annotations are accessible via 'Conserved Domain' links in Entrez.
  • The CD-Search service allows for the analysis of protein sequences against CDD models.
  • CDTree facilitates the examination of NCBI-curated domain hierarchies.

Conclusions:

  • CDD is a vital resource for protein sequence annotation and analysis.
  • CDTree enhances the utility of CDD by enabling detailed examination of domain relationships.
  • The integrated use of CDD and CDTree provides a powerful framework for protein classification based on domain family hierarchies.