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-protein Interfaces02:04

Protein-protein Interfaces

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 polypeptide...
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

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 polypeptide...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
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 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...

You might also read

Related Articles

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

Sort by
Same author

Simulation of cell-size systems at long timescales with flexible protein structures.

bioRxiv : the preprint server for biology·2026
Same author

Dockground: Expanding the Resource to Protein-DNA Complexes.

Journal of molecular biology·2025
Same author

Modeling CAPRI Targets of Round 55 by Combining AlphaFold and Docking.

Proteins·2025
Same author

GRAMMCell: Docking-based Cell Modeling Resource.

Journal of molecular biology·2025
Same author

Highly Optimized Simulation of Atomic Resolution Cell-Like Protein Environment.

The journal of physical chemistry. B·2025
Same author

Dockground: The Resource Expands to Protein-RNA Interactome.

Journal of molecular biology·2025

Related Experiment Video

Updated: May 8, 2026

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English
14:34

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

Published on: April 3, 2026

Global and local structural similarity in protein-protein complexes: implications for template-based docking.

Petras J Kundrotas1, Ilya A Vakser

  • 1Center for Bioinformatics, The University of Kansas, Lawrence, Kansas.

Proteins
|August 16, 2013
PubMed
Summary

Predicting protein-protein complex structures relies on structural similarity. This study reveals that interface similarity can be detected even with low sequence identity, offering broader template detection for protein docking.

Keywords:
bioinformaticsprotein modelingprotein recognitionstructural templatesstructure prediction

More Related Videos

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

Related Experiment Videos

Last Updated: May 8, 2026

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English
14:34

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

Published on: April 3, 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

Area of Science:

  • Structural Biology
  • Computational Biology
  • Bioinformatics

Background:

  • Protein-protein interactions are crucial for cellular functions.
  • Predicting protein complex structures is vital for understanding biological processes.
  • Large datasets of protein complex structures enable structure-based prediction methods.

Purpose of the Study:

  • To investigate the extent of structural similarity that allows for the detection of diverse templates in protein complex structure prediction.
  • To analyze the performance of interface-only versus full-structure alignment in identifying homologous protein-protein complexes.
  • To understand the relationship between sequence identity and structural similarity at protein-protein interfaces.

Main Methods:

  • Analysis of target-template similarity using a large dataset of heterodimeric protein complexes.
  • Comparison of structural alignment strategies focusing on interface regions versus entire protein structures.
  • Evaluation of similarity metrics including biological and crystal packing interfaces, and local structural motifs.

Main Results:

  • Structural similarity confined to protein-protein interfaces was found in approximately 25% of target-template pairs with less than 20% sequence identity, particularly with homodimeric templates.
  • In about 50% of cases, interface similarity was accompanied by overall structural similarity, with interface similarity being more pronounced.
  • Dissimilar interface structural motifs were observed even in overall similar protein structures.

Conclusions:

  • Structural similarity at protein-protein interfaces can be detected even with low sequence identity, expanding the scope of template detection for protein docking.
  • Interface-based structural alignment is a valuable strategy, especially when sequence identity is low.
  • The findings provide insights into the structural diversity of protein complexes and the effectiveness of different alignment approaches in predicting their structures.