Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

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...
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...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Membrane Domains01:18

Membrane Domains

The membrane domains concentrate specific lipids and proteins at one place within the membrane, which helps in cell signaling, adhesion, and other critical cellular processes. These domains can differ in size, composition, function, and lifespan.
Protein Domains
The membrane comprises a group of distinct proteins responsible for carrying out a cell's specific function. For example, the plasma membrane of the human sperm, or a single germ cell, contains a unique set of proteins in the anterior...
Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
Three-Domain System of Life01:21

Three-Domain System of Life

Ribosomal RNA (rRNA) sequence analysis revealed three distinct groups of cells: eukaryotes, bacteria, and archaea. In 1978, Carl R. Woese proposed the concept of domains, a taxonomic level above kingdoms, to differentiate these groups. He suggested that archaea and bacteria, despite their similar appearance, represent separate domains. Domains differ in rRNA, membrane lipid structure, transfer RNA, and antibiotic sensitivity.In this classification, animals, plants, and fungi belong to the...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Lycopene pathway rewiring by combinatorial co-expression of constituent enzymes in a cell-free protein synthesis system.

New biotechnology·2026
Same author

Vascular RhoJ Is an Effective and Selective Target for Tumor Angiogenesis and Vascular Disruption.

Cancer cell·2026
Same author

Hierarchical ceria nanoarchitecture enabling accelerated lattice oxygen activation for efficient redox reactions.

Nature communications·2026
Same author

De novo identification of potent ingredients for proteasome activation in MT101-5 using an AI-driven approach.

Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie·2026
Same author

SOCAR: Network-Based Computational Framework to Overcome Acquired Tamoxifen Resistance of MCF7 Cells.

IEEE transactions on computational biology and bioinformatics·2025
Same author

1,4-Naphthoquinone improves depressive-like behaviors by modulating neuronal factors and neuroinflammatory mediators.

Pharmacology, biochemistry, and behavior·2025

Related Experiment Video

Updated: Jun 18, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Protein comparison at the domain architecture level.

Byungwook Lee1, Doheon Lee

  • 1Korean BioInformation Center, KRIBB, Daejeon 305-806, Korea. bulee@kribb.re.kr

BMC Bioinformatics
|December 5, 2009
PubMed
Summary

We developed Weighed Domain Architecture Comparison (WDAC) to improve protein homology identification. This method effectively identifies homologous multidomain proteins by weighting domain architecture similarity.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Protein function is often inferred from homologous proteins.
  • Homology detection uses sequence-based or domain-based methods.
  • Domain-based methods struggle with promiscuous domains in large protein families.

Purpose of the Study:

  • To develop a novel method for identifying homologous multidomain proteins.
  • To improve the accuracy of homology detection, especially for proteins with mobile domains.

Main Methods:

  • Introduced Weighed Domain Architecture Comparison (WDAC) for domain architecture similarity.
  • Assigned weight scores to Pfam domains based on abundance and versatility.
  • Utilized cosine similarity to measure domain architecture similarity.

More Related Videos

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

Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing
12:04

Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing

Published on: October 3, 2018

Related Experiment Videos

Last Updated: Jun 18, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

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

Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing
12:04

Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing

Published on: October 3, 2018

  • Combined sequence similarity with domain architecture comparison.

    • Main Results:

    • WDAC demonstrated superior performance in identifying homology among multidomain proteins compared to unweighted methods.
    • Weighting domain architecture improved the detection of distant homology.
    • WDAC effectively distinguishes homologous proteins within large families.

    Conclusions:

    • Incorporating domain weight scores enhances protein homology identification accuracy.
    • WDAC offers a robust approach for analyzing multidomain protein families.
    • A web server is available for users to compare protein domain architectures.