Related Experiment Video
Updated: May 24, 2026
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
DOMIRE: a web server for identifying structural domains and their neighbors in proteins
Franck Samson1, Richard Shrager, Chin-Hsien Tai
1Institut National de la Recherche Agronomique, UR1077, Unité Mathématique, Informatique et Génome, 78350 Jouy-en-Josas, France.
Bioinformatics (Oxford, England)
|February 21, 2012
Summary
The DOMIRE web server automatically assigns protein structural domains using 3D substructure analysis. This tool aids in identifying protein common cores and understanding evolutionary relationships.
Area of Science:
- Structural bioinformatics
- Computational biology
- Protein science
Background:
- Protein domain assignment is crucial for understanding protein function and evolution.
- Existing methods may lack automation or comprehensive analysis.
- The DOMIRE web server provides a novel approach to protein domain analysis.
Purpose of the Study:
- To develop and present the DOMIRE web server, a tool for automatic protein structural domain assignment.
- To offer insights into protein domain organization and evolutionary relationships.
Main Methods:
- Utilizes a novel, automatic procedure for protein structural domain assignment.
- Employs 3D substructure comparison against a non-redundant protein database.
- Transforms common 3D substructures into a co-occurrence matrix for global domain view.
- Applies three algorithms to define structural domain boundaries from the co-occurrence matrix.
Main Results:
- DOMIRE successfully assigns protein structural domains based on shared 3D substructures.
- Generates a co-occurrence matrix for visualizing protein domain organization.
- Provides lists of structural neighbors and their alignments for each query.
- Demonstrates utility in identifying protein common cores.
Conclusions:
- DOMIRE is a valuable web server for automatic protein structural domain assignment.
- Facilitates the definition of protein common cores and the study of evolutionary relationships.
- Offers a global perspective on protein domain organization through its co-occurrence matrix approach.
More Related Videos
Related Concept Videos
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...
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.
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.
01:13Protein Organization
Overview
01:13Protein Organization
Overview
01:56Structural Protein Function
Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity. In bones and teeth, it mineralizes to form...
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity. In bones and teeth, it mineralizes to form...