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

Protein Organization01:24

Protein Organization

8.8K
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....
8.8K
Protein and Protein Structure02:15

Protein and Protein Structure

86.2K
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...
86.2K

You might also read

Related Articles

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

Sort by
Same author

Development and comparison of evaluation metrics for batch correction reveals performance differences.

Bioinformatics advances·2026
Same author

On the state of protein function prediction: a report on the fourth CAFA challenge.

bioRxiv : the preprint server for biology·2026
Same author

Recruitment of bifunctional regulator thermospermine to methylated ribosomes directs xylem fate.

Science (New York, N.Y.)·2026
Same author

3-D substructure search by transitive closure in AlphaFold database.

Protein science : a publication of the Protein Society·2025
Same author

Mitotic abnormalities precede microsatellite instability in lynch syndrome-associated colorectal tumourigenesis.

EBioMedicine·2024
Same author

Global analysis of aging-related protein structural changes uncovers enzyme-polymerization-based control of longevity.

Molecular cell·2023
Same journal

Mapping the 3D Chromosome Organization of a Biosynthetic Gene Cluster by Capture Hi-C (CHi-C).

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Mapping the 3D Chromosome Organization of Streptomyces by Hi-C.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

CUT&Tag Epigenomic Profiling of Biosynthetic Gene Clusters in Arabidopsis thaliana.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Rhizobium rhizogenes-Mediated Hairy Root Transformation Protocol for Lotus japonicus and Other Legumes.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Characterization of Bioactive Saponins from Sea Cucumbers.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Methods for Functional Validation of Terpenoid Metabolic Clusters in Nicotiana benthamiana and Aspergillus oryzae.

Methods in molecular biology (Clifton, N.J.)·2026
See all related articles

Related Experiment Video

Updated: Dec 29, 2025

Contrast-Matching Detergent in Small-Angle Neutron Scattering Experiments for Membrane Protein Structural Analysis and Ab Initio Modeling
10:27

Contrast-Matching Detergent in Small-Angle Neutron Scattering Experiments for Membrane Protein Structural Analysis and Ab Initio Modeling

Published on: October 21, 2018

12.9K

Using Dali for Protein Structure Comparison.

Liisa Holm1

  • 1Faculty of Biological and Environmental Sciences and Institute of Biotechnology, University of Helsinki, Helsinki, Finland. liisa.holm@helsinki.fi.

Methods in Molecular Biology (Clifton, N.J.)
|February 2, 2020
PubMed
Summary
This summary is machine-generated.

The Distance matrix alignment (Dali) tool helps classify new protein structures by comparing them to existing ones. This method is crucial for organizing the rapidly growing database of solved protein structures.

Keywords:
Classification of protein foldsDatabase searchingDistance geometryPattern recognitionProtein structure alignment

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

15.9K
Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

2.4K

Related Experiment Videos

Last Updated: Dec 29, 2025

Contrast-Matching Detergent in Small-Angle Neutron Scattering Experiments for Membrane Protein Structural Analysis and Ab Initio Modeling
10:27

Contrast-Matching Detergent in Small-Angle Neutron Scattering Experiments for Membrane Protein Structural Analysis and Ab Initio Modeling

Published on: October 21, 2018

12.9K
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

15.9K
Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

2.4K

Area of Science:

  • Structural biology
  • Bioinformatics

Background:

  • The increasing number of solved protein structures necessitates efficient classification and correlation methods.
  • Structural data analysis is vital for understanding protein function and evolution.

Purpose of the Study:

  • To highlight the utility of Distance matrix alignment (Dali) for structural bioinformatics.
  • To provide accessible resources for protein structure comparison.

Main Methods:

  • Utilizing Distance matrix alignment (Dali) for pairwise structural comparisons.
  • Employing a web server for easy access to Dali functionality.
  • Offering local download for Linux users to perform comparisons.

Main Results:

  • Dali is a routine tool for crystallographers to screen structural databases.
  • The Dali web server provides accessible protein structure similarity searches.
  • Local Dali installation allows for on-premises structural comparisons.

Conclusions:

  • Distance matrix alignment (Dali) is an essential tool for managing and classifying protein structural data.
  • Web-based and local versions of Dali enhance accessibility for researchers worldwide.