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

Assembly of Signaling Complexes01:30

Assembly of Signaling Complexes

Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
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...
Anchoring Junctions01:03

Anchoring Junctions

Anchoring junctions are multiprotein complexes that help cells connect to other cells and the extracellular matrix. Anchoring junctions are present on the lateral and basal surfaces of cells, providing strong and flexible connections. Focal adhesions are often formed due to cell interactions with the ECM substrata, which initiate signal transduction via kinase cascades and other mechanisms. Together, they provide stability and tissue integrity. There are three types of anchoring junctions:...
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...

You might also read

Related Articles

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

Sort by
Same author

Molecular mechanisms of the MLL4 complex in H3K4 methylation and p53-dependent transcription activation.

Molecular cell·2026
Same author

CliPepPI: Scalable prediction of domain-peptide specificity using contrastive learning.

bioRxiv : the preprint server for biology·2026
Same author

CSN5i-3 is an orthosteric molecular glue inhibitor of COP9 signalosome.

Nature·2026
Same author

Orthosteric Molecular Glue Inhibits COP9 Signalosome with Substrate-Dependent Potency.

bioRxiv : the preprint server for biology·2025
Same author

Calibrated Variant Effect Prediction at the Residue Level Using Conditional Score Distributions.

bioRxiv : the preprint server for biology·2025
Same author

Cysteine-enabled cleavability to advance cross-linking mass spectrometry for global analysis of endogenous protein-protein interactions.

Nature communications·2025

Related Experiment Video

Updated: Jun 11, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

An integrated suite of fast docking algorithms.

Efrat Mashiach1, Dina Schneidman-Duhovny, Aviyah Peri

  • 1Raymond and Beverly Sackler Faculty of Exact Sciences, Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel.

Proteins
|July 8, 2010
PubMed
Summary
This summary is machine-generated.

This study presents a comprehensive docking protocol for predicting molecular interactions. Integrating biological data and refinement significantly improved prediction accuracy in protein-protein docking challenges.

More Related Videos

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

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 11, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

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

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:

  • Computational biology
  • Structural bioinformatics
  • Molecular modeling

Background:

  • The Critical Assessment of Predicted Interactions (CAPRI) experiment provides realistic challenges for molecular docking algorithms.
  • Developing robust docking algorithms is crucial for understanding protein-protein interactions and drug discovery.

Purpose of the Study:

  • To develop and implement a comprehensive suite of docking algorithms integrated into a dynamic protocol.
  • To enhance the accuracy and success rate of predicting molecular interactions, particularly protein-protein complexes.

Main Methods:

  • A four-stage dynamic docking protocol: (1) biological and bioinformatics research for site prediction and constraint definition, (2) rigid/flexible docking (PatchDock, FlexDock) and symmetric complex prediction (SymmDock), (3) flexible refinement and reranking (FiberDock), and (4) clustering and filtering.
  • Utilizing gathered biological information to guide docking and employing refinement stages to improve solution ranking.

Main Results:

  • The protocol demonstrated improved performance on benchmark datasets and recent CAPRI targets.
  • Incorporating biological information prior to docking significantly increased the success rate.
  • The refinement and rescoring stage notably improved the ranking of rigid docking solutions.

Conclusions:

  • Biological information gathering and a dedicated refinement stage are critical for successful molecular docking.
  • Failures were often linked to handling backbone flexibility, homology modeling inaccuracies, or incorrect biological assumptions.
  • The developed methods are largely available for use in further research.