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Related Concept Videos

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...
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...
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

CDD: conserved domains and protein three-dimensional structure.

Aron Marchler-Bauer1, Chanjuan Zheng, Farideh Chitsaz

  • 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
|December 1, 2012
PubMed
Summary

The Conserved Domain Database (CDD) annotates protein sequences with conserved domain footprints and functional sites. It uses RPS-BLAST for rapid identification and incorporates curated protein domain families, including 3D structures.

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Area of Science:

  • Bioinformatics
  • Structural Biology
  • Computational Biology

Background:

  • The Conserved Domain Database (CDD) is a crucial resource within NCBI's Entrez system.
  • It provides annotations for protein sequences, identifying conserved domain footprints and functional sites.

Purpose of the Study:

  • To describe the features and accessibility of the Conserved Domain Database (CDD).
  • To highlight CDD's role in protein sequence annotation and classification.

Main Methods:

  • Utilizes RPS-BLAST for rapid identification of putative protein sequence matches.
  • Incorporates multiple protein domain and full-length protein model collections.
  • Leverages protein three-dimensional (3D) structures and published literature for curation.

Main Results:

  • CDD offers pre-computed annotations via Entrez and interactive search services.
  • Supports single and batch submissions for protein and nucleotide queries.
  • The majority of protein 3D structures are represented by models tracked by CDD.

Conclusions:

  • CDD provides a comprehensive resource for understanding protein domain organization and function.
  • Active curation efforts enhance the classification of protein families, especially those supported by structural data.
  • CDD plays a vital role in characterizing novel protein families emerging from structural biology research.