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Related Concept Videos

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...
Genome Annotation and Assembly03:36

Genome 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.
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...
Multi-species Conserved Sequences02:51

Multi-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...

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Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances
07:35

Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances

Published on: October 11, 2018

CDD: specific functional annotation with the Conserved Domain Database.

Aron Marchler-Bauer1, John B Anderson, 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
|November 6, 2008
PubMed
Summary
This summary is machine-generated.

The Conserved Domain Database (CDD) annotates protein sequences with conserved domain information. Version 2.14 introduces superfamily-level summaries and flags annotations as specific or non-specific for improved accuracy.

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Area of Science:

  • Bioinformatics
  • Structural Biology
  • Computational Biology

Background:

  • The Conserved Domain Database (CDD) at NCBI is a vital resource for identifying conserved protein domains.
  • It aids in understanding protein evolution and function through sequence alignments and search models.

Purpose of the Study:

  • To describe the NCBI Conserved Domain Database (CDD) and its functionalities.
  • To highlight updates in CDD version 2.14, including superfamily-level summarization and refined annotation flagging.

Main Methods:

  • The CDD integrates multiple sequence alignments and database search models.
  • It provides precalculated domain annotations for sequences in the Entrez system.
  • The CD-Search service allows querying novel protein sequences against the CDD models.

Main Results:

  • CDD offers annotation of domain footprints and conserved functional sites on protein sequences.
  • CDD v2.14 summarizes redundant and homologous domain models at a superfamily level.
  • Annotations are now flagged as 'specific' (high confidence molecular function) or 'non-specific' (superfamily membership).

Conclusions:

  • The enhanced CDD provides more nuanced and accurate domain annotation for protein sequences.
  • These improvements facilitate a better understanding of protein function and evolutionary relationships.
  • CDD remains a crucial tool for researchers in molecular biology and bioinformatics.