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

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.
Protein Organization01:24

Protein 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.
Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...
Protein and Protein Structures02:15

Protein 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...
Protein and Protein Structure02:15

Protein 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...
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...

You might also read

Related Articles

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

Sort by
Same author

Extending structural surfaceomics to identify aberrant conformations of tumor surface proteins as potential immunotherapy targets.

bioRxiv : the preprint server for biology·2026
Same author

Systematic discovery of pro- and anti-HIV host factors in primary human CD4+ T cells.

Cell·2026
Same author

The scientific legacy of Martin Karplus from the perspective of his collaborators.

Biophysical journal·2026
Same author

The filamentous ultrastructure of the PopZ condensate is required for its cellular function.

Nature structural & molecular biology·2026
Same author

ModelCIF Update: Supporting Emerging Classes of Computational Macromolecular Models.

Journal of molecular biology·2026
Same author

IHMValidation: Assessment of Integrative Structure Models Deposited to the Protein Data Bank.

Journal of molecular biology·2025

Related Experiment Video

Updated: May 22, 2026

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

SALIGN: a web server for alignment of multiple protein sequences and structures.

Hannes Braberg1, Benjamin M Webb, Elina Tjioe

  • 1Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA.

Bioinformatics (Oxford, England)
|May 24, 2012
PubMed
Summary

The SALIGN web server provides accurate protein sequence and structure alignment for biological analyses like functional annotation and protein family classification. It offers automated alignment procedures with user-adjustable parameters for enhanced accuracy.

More Related Videos

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

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

Related Experiment Videos

Last Updated: May 22, 2026

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

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

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

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Accurate protein alignment is essential for functional annotation, protein family classification, and comparative protein structure modeling.
  • The SALIGN web server, a module of the MODELLER software, offers a versatile tool for protein multiple sequence/structure alignment.
  • Both SALIGN and MODELLER are freely accessible to the academic community.

Purpose of the Study:

  • To introduce a web interface for SALIGN, a protein multiple sequence/structure alignment module.
  • To provide automated alignment procedures that can be customized by users.
  • To enhance accuracy in protein alignment for various biological analyses.

Main Methods:

  • The SALIGN web server automatically selects alignment procedures based on input data.
  • Multiple sequence alignments are guided by dendrograms derived from pairwise alignment scores.
  • Sequence-to-structure alignments utilize structural environment information for optimal gap placement.
  • Profile-profile alignment is performed when two multiple sequence alignments of related proteins are provided.

Main Results:

  • The SALIGN web server offers an automated yet customizable approach to protein alignment.
  • It incorporates advanced methods like dendrogram-guided multiple alignments and structure-aware gap placement.
  • The server supports profile-profile alignment for related protein sets.

Conclusions:

  • The SALIGN web server enhances the accuracy of protein sequence and structure alignment.
  • Its features are optimized for applications in comparative modeling and identifying protein interaction partners.
  • This tool facilitates critical biological analyses, improving functional annotation and classification accuracy.