Jove
Visualize
Contact Us

Related Concept Videos

Protein Organization01:24

Protein Organization

6.0K
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....
6.0K
Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

42.9K
Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
42.9K
Protein Networks02:26

Protein Networks

3.9K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
3.9K
Protein-protein Interfaces02:04

Protein-protein Interfaces

12.4K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
12.4K
Protein and Protein Structure02:15

Protein and Protein Structure

77.2K
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...
77.2K

You might also read

Related Articles

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

Sort by
Same author

Novel monoclonal antibodies for immunodetection of AmpC β-lactamases.

PeerJ·2025
Same author

Evidence for the Pathogenicity of a <i>CFH</i> Variant in a Multigenerational Family with Cuticular Drusen.

Medicina (Kaunas, Lithuania)·2025
Same author

FTDMP: A Framework for Protein-Protein, Protein-DNA, and Protein-RNA Docking and Scoring.

Proteins·2025
Same author

GTalign: spatial index-driven protein structure alignment, superposition, and search.

Nature communications·2024
Same author

PPI3D: a web server for searching, analyzing and modeling protein-protein, protein-peptide and protein-nucleic acid interactions.

Nucleic acids research·2024
Same author

Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment.

Proteins·2023
Same journal

Correction to 'scSuperAnnotator: A platform for benchmarking comparison and visualizing automated cellular annotation methods for scRNA-seq data'.

Nucleic acids research·2026
Same journal

Correction to 'Differentiable partition function calculation for RNA'.

Nucleic acids research·2026
Same journal

Deployment of non-canonical splicing in tunicate genomes is mediated by divergent U2AF function and changing m6A modification in U1 and U6 snRNA.

Nucleic acids research·2026
Same journal

Bacillus subtilis DnaB forms multiple protein-protein interactions essential for DNA replication initiation.

Nucleic acids research·2026
Same journal

Multiple forms of protein-protein and DNA binding are exhibited by BrxC from the BREX phage restriction system.

Nucleic acids research·2026
Same journal

Biosynthesis of glycosylated 5-hydroxycytosine in the DNA of diverse viruses.

Nucleic acids research·2026
See all related articles
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 Experiment Video

Updated: May 8, 2025

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

68.4K

Web-based GTalign: bridging speed and accuracy in protein structure analysis.

Justas Dapkūnas1, Mindaugas Margelevičius1

  • 1Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, 10257 Vilnius, Lithuania.

Nucleic Acids Research
|May 7, 2025
PubMed
Summary
This summary is machine-generated.

GTalign-web offers accurate and fast protein structure alignment, aiding in understanding protein relationships and annotating unknown proteins. This web tool enhances structural biology research and functional genomics.

More Related Videos

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

7.0K
An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

3.3K

Related Experiment Videos

Last Updated: May 8, 2025

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

68.4K
Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

7.0K
An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

3.3K

Area of Science:

  • Structural biology
  • Bioinformatics
  • Computational biology

Background:

  • Accurate protein structure alignment is critical for deciphering protein structure-function relationships and evolutionary connections.
  • Existing tools may face limitations in speed or accuracy for large-scale structural analyses.
  • The need for accessible, high-performance tools for protein structure comparison is ongoing.

Purpose of the Study:

  • To introduce GTalign-web, a web-based platform for GTalign, a spatial index-driven protein structure alignment tool.
  • To provide a user-friendly and high-performance solution for structural searches and functional annotation of proteins.
  • To evaluate GTalign-web's performance against established structural alignment servers.

Main Methods:

  • Development of GTalign-web as a web implementation of the GTalign algorithm.
  • Utilizing a spatial index for efficient structural searching.
  • Benchmarking GTalign-web against DALI and Foldseek using established datasets and metrics.
  • Application of GTalign-web for annotating uncharacterized proteins against the UniRef30 database.

Main Results:

  • GTalign-web demonstrates superior accuracy compared to DALI and Foldseek servers.
  • The tool achieves rapid search times, indicating high performance.
  • Successful annotation of uncharacterized proteins using GTalign-web, highlighting its practical utility.
  • The web server provides a valuable resource for structural and functional protein analysis.

Conclusions:

  • GTalign-web is an accurate and efficient tool for protein structure alignment and functional annotation.
  • The web-based implementation enhances accessibility for researchers in structural biology and bioinformatics.
  • GTalign-web serves as a valuable resource for exploring protein structural similarities and inferring functions.