Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Conservation of Protein Domains02:26

Conservation of Protein Domains

3.2K
3.2K
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

11.1K
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...
11.1K
Conserved Binding Sites01:49

Conserved Binding Sites

4.3K
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...
4.3K
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

4.0K
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...
4.0K
Three-Domain System of Life01:21

Three-Domain System of Life

113
Ribosomal RNA (rRNA) sequence analysis revealed three distinct groups of cells: eukaryotes, bacteria, and archaea. In 1978, Carl R. Woese proposed the concept of domains, a taxonomic level above kingdoms, to differentiate these groups. He suggested that archaea and bacteria, despite their similar appearance, represent separate domains. Domains differ in rRNA, membrane lipid structure, transfer RNA, and antibiotic sensitivity.In this classification, animals, plants, and fungi belong to the...
113
Membrane Domains01:18

Membrane Domains

5.6K
The membrane domains concentrate specific lipids and proteins at one place within the membrane, which helps in cell signaling, adhesion, and other critical cellular processes. These domains can differ in size, composition, function, and lifespan.
Protein Domains
The membrane comprises a group of distinct proteins responsible for carrying out a cell's specific function. For example, the plasma membrane of the human sperm, or a single germ cell, contains a unique set of proteins in the...
5.6K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Elucidating the interaction between pyrazine flavor compounds and coffee proteins: Insights from multiscale structural and molecular dynamics simulations.

Current research in food science·2026
Same author

Angelica dahurica alleviates migraine via ameliorating neuroinflammation and oxidative stress.

Journal of ethnopharmacology·2026
Same author

Pilot Study of Gallic Acid Cream as a Potential Treatment for Plaque Psoriasis.

Journal of medicinal food·2026
Same author

STNAGNN: Data-driven Spatio-temporal Brain Connectivity beyond FC.

Proceedings of machine learning research·2026
Same author

<i>MFAP2</i> Promotes Glioblastoma Malignant Phenotypes via Autophagy-Dependent Activation of Wnt/β-Catenin Signaling.

Biomedicines·2026
Same author

Sexual Dimorphism in the Relationship between Body Composition and Insulin Resistance in Older Adults.

Current developments in nutrition·2026
Same journal

Correction to 'New origin firing is inhibited by APC/CCdh1 activation in S-phase after severe replication stress'.

Nucleic acids research·2026
Same journal

VeloRM: disentangling pre- and post-splicing RNA modification dynamics at single-cell resolution.

Nucleic acids research·2026
Same journal

Accessibility of telomeric overhangs to stabilizing small-molecule ligands.

Nucleic acids research·2026
Same journal

Multivalent interactions mediate SNAIL transcription factor stimulation of the nucleosome deacetylase activity of the CoREST complex.

Nucleic acids research·2026
Same journal

Genome-wide mapping of DNA G-quadruplexes in Trypanosoma brucei chromatin reveals enrichment in coding regions and transcription start sites.

Nucleic acids research·2026
Same journal

Correction to 'The Gene Ontology knowledgebase in 2026'.

Nucleic acids research·2026
See all related articles

Related Experiment Video

Updated: Aug 18, 2025

Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing
12:04

Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing

Published on: October 3, 2018

9.0K

The conserved domain database in 2023.

Jiyao Wang1, Farideh Chitsaz1, Myra K Derbyshire1

  • 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.

Nucleic Acids Research
|December 8, 2022
PubMed
Summary
This summary is machine-generated.

The National Library of Medicine's Conserved Domain Database (CDD) annotates protein sequences with functional information. It addresses challenges in maintaining comprehensive protein domain models and aims to improve annotation for uncharacterized proteins.

More Related Videos

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
16:02

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Published on: February 10, 2023

2.8K
Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C
09:32

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C

Published on: October 14, 2022

3.6K

Related Experiment Videos

Last Updated: Aug 18, 2025

Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing
12:04

Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing

Published on: October 3, 2018

9.0K
Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
16:02

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Published on: February 10, 2023

2.8K
Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C
09:32

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C

Published on: October 14, 2022

3.6K

Area of Science:

  • Bioinformatics
  • Structural Biology
  • Genomics

Background:

  • The National Library of Medicine's Conserved Domain Database (CDD) is a public resource of protein domain and family models.
  • It has been available for over 20 years, accumulating a substantial collection of curated data.
  • Maintaining and releasing updated annotations has faced challenges due to the growing archive of pre-computed data.

Purpose of the Study:

  • To provide functional annotation for protein and translated nucleotide sequences.
  • To define protein domain architecture for assigning gene product names and functions.
  • To address challenges in releasing updated CDD models and improve annotation for uncharacterized proteins.

Main Methods:

  • Construction of protein domain and family models using multiple sequence alignments.
  • Hierarchical classification of large protein domain families.
  • Surveillance of unannotated proteins ('dark matter') to add new domain models.
  • Efforts to name and attribute conserved domain architectures.

Main Results:

  • The CDD provides location of domain footprints and functional sites on sequences.
  • It defines protein domain architecture, aiding in gene product naming and function prediction.
  • Ongoing curation efforts focus on novel domain families and conserved domain architectures.

Conclusions:

  • The CDD is a vital resource for protein sequence annotation and functional prediction.
  • Challenges in data maintenance have impacted release frequency, but curation efforts continue.
  • The database plays a crucial role in understanding protein function and evolution.