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...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
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...
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,...

You might also read

Related Articles

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

Sort by
Same author

Effects of a psychoeducation program for relatives of patients with first-episode psychosis who have received psychoeducation: An observational study.

L'Encephale·2026
Same author

Challenges in predicting PROTAC-mediated protein-protein interfaces with AlphaFold reveal a general limitation on small interfaces.

Bioinformatics advances·2025
Same author

Dynamics of Protein-RNA Interfaces Using All-Atom Molecular Dynamics Simulations.

The journal of physical chemistry. B·2024
Same author

AlphaFold2 Predicts Whether Proteins Interact Amidst Confounding Structural Compatibility.

Journal of chemical information and modeling·2024
Same author

Values for the Digestibility of Pea Protein Isolate or Casein Amino Acids Determined using the Dual Isotope Method Are Not Similar to Those Derived with the Standard Ileal Balance Method in Healthy Volunteers.

The Journal of nutrition·2023
Same author

Rational Prediction of PROTAC-Compatible Protein-Protein Interfaces by Molecular Docking.

Journal of chemical information and modeling·2023
Same journal

Correction to: Long range Debye-Hückel correction for computation of grid-based electrostatic forces between biomacromolecules.

BMC biophysics·2020
Same journal

Covalent linkage of bacterial voltage-gated sodium channels.

BMC biophysics·2019
Same journal

Role of protein interactions in stabilizing canonical DNA features in simulations of DNA in crowded environments.

BMC biophysics·2018
Same journal

A discontinuous Galerkin model for fluorescence loss in photobleaching of intracellular polyglutamine protein aggregates.

BMC biophysics·2018
Same journal

Phenylalanine intercalation parameters for liquid-disordered phase domains - a membrane model study.

BMC biophysics·2018
Same journal

Jörg Langowski: his scientific legacy and the future it promises.

BMC biophysics·2018
See all related articles

Related Experiment Video

Updated: May 22, 2026

Protein Target Prediction and Validation of Small Molecule Compound
10:21

Protein Target Prediction and Validation of Small Molecule Compound

Published on: February 23, 2024

Arbitrary protein-protein docking targets biologically relevant interfaces.

Juliette Martin1, Richard Lavery

  • 1Université Lyon 1; CNRS, UMR 5086; Bases Moléculaires et Structurales des Systèmes Infectieux, IBCP, 7 passage du, Vercors, F-69367, France. Juliette.Martin@ibcp.fr.

BMC Biophysics
|May 8, 2012
PubMed
Summary
This summary is machine-generated.

Arbitrary docking of proteins reveals that even random partners interact non-randomly at specific sites. This physical property helps predict biologically relevant protein interfaces, improving our understanding of protein-protein recognition.

More Related Videos

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

Related Experiment Videos

Last Updated: May 22, 2026

Protein Target Prediction and Validation of Small Molecule Compound
10:21

Protein Target Prediction and Validation of Small Molecule Compound

Published on: February 23, 2024

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

Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • Protein-protein interactions are crucial for biological processes.
  • Distinguishing true from false protein complexes in cross-docking experiments is challenging.
  • False complexes may indicate weak or non-specific interactions.

Purpose of the Study:

  • Investigate the 'twilight zone' of protein-protein interactions.
  • Determine if randomly docked protein partners exhibit non-random binding patterns.
  • Assess the potential of arbitrary docking for predicting biologically relevant protein interfaces.

Main Methods:

  • Performed arbitrary docking using a dataset of 198 proteins and over 300 random probe proteins.
  • Analyzed the localization, shape, and composition of generated protein-protein interfaces.
  • Evaluated the predictive power of arbitrary docking for identifying binding sites.

Main Results:

  • Arbitrary protein docking demonstrates a generic tendency for partners to aggregate at localized surface regions.
  • Generated interfaces are not systematically planar or curved but are closer to protein centers.
  • Arbitrary docking alone predicted biological interfaces with an AUC of 0.69, improving to 0.72 with evolutionary information.

Conclusions:

  • Arbitrary docking, based on physical properties, can effectively identify biologically relevant protein interfaces.
  • This method offers a computationally practical approach to understanding protein interactions.
  • Nonspecific interfaces identified through arbitrary docking can highlight alternative binding sites.