Related Experiment Video
Updated: Jun 1, 2026
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein
Corin Yeats1, Jonathan Lees, Phil Carter
1Research Department of Structural and Molecular Biology, Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower St, London. WC1E 6BT, UK. yeats@biochem.ucl.ac.uk
Nucleic Acids Research
|June 8, 2011
Summary
Gene3D offers structural domain annotations for millions of proteins, integrating diverse biological data. Web services provide easy access to this information for analyzing novel protein sequences and understanding domain architectures.
Area of Science:
- Structural bioinformatics
- Genomics
- Proteomics
Background:
- The Gene3D database curates structural domain annotations for over 7 million proteins.
- Annotations are based on the CATH structural domain superfamilies and integrated with external data.
- Existing resources lack comprehensive, easily accessible protein domain information.
Purpose of the Study:
- To provide programmatic access to the integrated Gene3D database.
- To offer tools for analyzing novel protein sequences.
- To facilitate integration of domain annotations into local analysis pipelines.
Main Methods:
- Construction of web services for programmatic database access.
- Integration of functional, genomic, and molecular data from resources like GO, EC, UniProt, and NCBI Taxonomy.
- Development of the Gene3D domain recognition tool (Gene3DScan) and a protein sequence annotation pipeline.
Main Results:
- Web services provide access to domain annotations for 7 million proteins.
- Integrated data includes functional, genomic, and molecular information.
- Tools are available for analyzing novel protein sequences and retrieving specific data, such as GO terms or multi-domain architectures.
Conclusions:
- The Gene3D web services offer a flexible means to integrate domain annotations and associated data.
- Programmatic access simplifies the incorporation of protein domain information into local analysis software.
- These services enhance the utility of the Gene3D database for researchers in structural bioinformatics and genomics.
Related Concept Videos
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.
02:15Protein and Protein Structures
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...
A protein's shape is critical to its function. For example, an enzyme can...
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...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
02:15Protein and Protein Structure
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...
A protein's shape is critical to its function. For example, an enzyme can...
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...
01:24Protein 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.
The primary structure of a protein is its amino acid sequence.