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

Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

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...
Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

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...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
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...
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...

You might also read

Related Articles

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

Sort by
Same author

Mutations in LZTR1 drive human disease by dysregulating RAS ubiquitination.

Science (New York, N.Y.)·2018
Same author

Contribution of salt bridges toward protein thermostability.

Journal of biomolecular structure & dynamics·2012
Same author

Towards drugs targeting multiple proteins in a systems biology approach.

Current topics in medicinal chemistry·2007
Same author

MASS: multiple structural alignment by secondary structures.

Bioinformatics (Oxford, England)·2003
Same author

Transient, highly populated, building blocks folding model.

Cell biochemistry and biophysics·2002
Same author

Building blocks, hinge-bending motions and protein topology.

Journal of biomolecular structure & dynamics·2002

Related Experiment Video

Updated: Jun 4, 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

GOSSIP: a method for fast and accurate global alignment of protein structures.

I Kifer1, R Nussinov, H J Wolfson

  • 1School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Sackler Institute of Molecular Medicine, Tel Aviv University, Tel Aviv, Israel.

Bioinformatics (Oxford, England)
|February 8, 2011
PubMed
Summary

A new method called GOSSIP enables rapid, global, all-against-all alignment of protein structures. This tool efficiently identifies similar protein structures, outperforming existing methods in speed without sacrificing accuracy.

More Related Videos

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

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

Related Experiment Videos

Last Updated: Jun 4, 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

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

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

Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Biochemistry

Background:

  • The Protein Data Bank (PDB) is rapidly expanding, necessitating efficient methods for analyzing vast structural data.
  • Existing protein structure comparison tools often focus on local alignments, which are computationally intensive and slow for large-scale analysis.
  • There is a growing need for fast tools to identify similar structures and cluster them based on structural resemblance.

Purpose of the Study:

  • To develop a novel computational method for fast, global, all-against-all alignment of protein structures.
  • To enable efficient analysis of large datasets of protein structures by identifying similarities at a high speed.
  • To provide a tool that overcomes the limitations of local alignment methods for large-scale structural comparisons.

Main Methods:

  • Introduction of GOSSIP (Global Structure Similarity Identification Program), a novel method for global all-against-all protein structure alignment.
  • GOSSIP detects structural similarities down to a user-defined cutoff, facilitating rapid identification of related structures.
  • The method was evaluated on datasets of short structural fragments and large, sequence-diverse structural benchmarks.

Main Results:

  • GOSSIP achieves significantly higher speeds compared to existing local structure alignment methods and database scanning approaches.
  • The method demonstrates speed improvements of several orders of magnitude for comparing numerous structures.
  • Evaluations confirmed that for similarity thresholds of 0.6 and above, GOSSIP maintains accuracy in alignments and the number of detected global similarities.

Conclusions:

  • GOSSIP provides a computationally efficient solution for analyzing large protein structure datasets.
  • The method enables high-speed identification and clustering of structurally similar proteins without compromising accuracy.
  • GOSSIP is available as a server and downloadable executable, facilitating its use in structural bioinformatics research.