Related Experiment Video
Updated: May 23, 2026
16:41
A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Annotation of functional sites with the Conserved Domain Database
Myra K Derbyshire1, Christopher J Lanczycki, Stephen H Bryant
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.
Database : the Journal of Biological Databases and Curation
|March 22, 2012
Summary
The National Center for Biotechnology Information
Area of Science:
- Bioinformatics
- Computational Biology
- Structural Biology
Background:
- Most protein sequences lack experimental functional assessment.
- Functional annotation often relies on homology.
- Site-specific annotation offers detailed functional insights.
Purpose of the Study:
- To compare site annotations derived from conserved domain models with existing high-quality annotations.
- To evaluate the utility of the National Center for Biotechnology Information's Conserved Domain Database (CDD) for site annotation.
Main Methods:
- Utilized CDD's curated site annotations categorized into seven types.
- Performed comparative analysis of CDD-derived site annotations against existing datasets.
- Leveraged high-confidence domain matches for annotation transfer.
Main Results:
- CDD-based site annotation can cover substantial portions of protein sequences.
- CDD annotations complement existing site data, particularly for conserved sites across diverse species.
- Evidence from multiple 3D structures supports CDD curation practices.
Conclusions:
- Domain-based site annotation, particularly from CDD, is a valuable complement to existing functional annotations.
- This approach enhances the understanding of protein function and sequence variation.
- CDD facilitates the transfer of detailed functional site information across related protein sequences.
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...
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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.
00:49Ligand Binding and Linkage
Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked. In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...