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

14.2K
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...
14.2K
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

4.2K
4.2K
Protein Networks02:26

Protein Networks

4.3K
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,...
4.3K
Protein Networks02:26

Protein Networks

2.6K
2.6K
Conserved Binding Sites01:49

Conserved Binding Sites

4.8K
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...
4.8K
Ligand Binding Sites02:40

Ligand Binding Sites

14.5K
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...
14.5K

You might also read

Related Articles

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

Sort by
Same author

S1P-S1PR1 signaling impairs CD8<sup>+</sup> T cell metabolism and effector function in tumors.

EMBO reports·2026
Same author

The endoplasmic reticulum protein FAM134B acts as a regulator of mitochondrial morphology.

Journal of cell science·2025
Same author

Co-Var, a Measure to Determine Intra-protein, Inter-protein, Protein-DNA, or Protein-RNA Coevolution.

Methods in molecular biology (Clifton, N.J.)·2025
Same author

The impact of ER<sup>UPR</sup> on mitochondrial integrity mediated by PDK4.

Cell death & disease·2025
Same author

Dual-specific autophosphorylation of kinase IKK2 enables phosphorylation of substrate IκBα through a phosphoenzyme intermediate.

eLife·2025
Same author

Whole exome sequencing reveals novel and rare variants in nonsyndromic hearing loss-related genes: A focus on <i>GPSM2</i> compound heterozygosity.

Journal of biosciences·2025
Same journal

Therapeutic potential of crude protein extracts from two Egyptian freshwater snails Lanistes carinatus and Bellamya unicolor.

Scientific reports·2026
Same journal

Microbial contamination of donor corneas and post-keratoplasty endophthalmitis: a comparison between Japanese and U.S. eye banks using cold storage.

Scientific reports·2026
Same journal

Prevalence and contributing factors of virological non-suppression among adult patients on first-line antiretroviral therapy in tertiary hospitals in Ethiopia.

Scientific reports·2026
Same journal

An in vitro comparison of color stability between alkasite and different restorative materials in various staining solutions.

Scientific reports·2026
Same journal

Toward accessible mRNA LNP formulation: systematic evaluation of mixing strategies and key parameters.

Scientific reports·2026
Same journal

A network analysis of personality traits, mentalizing, and psychological health in Chinese college students.

Scientific reports·2026
See all related articles

Related Experiment Video

Updated: Nov 20, 2025

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

2.3K

Classification and prediction of protein-protein interaction interface using machine learning algorithm.

Subhrangshu Das1, Saikat Chakrabarti2

  • 1Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, WB, India.

Scientific Reports
|January 20, 2021
PubMed
Summary
This summary is machine-generated.

Computational methods predict protein-protein interaction interfaces. This study identifies key structural features to distinguish native from non-native complexes, improving accuracy for therapeutic target discovery.

More Related Videos

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells
08:38

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells

Published on: March 3, 2015

13.7K
Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA
10:21

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Published on: February 23, 2024

3.3K

Related Experiment Videos

Last Updated: Nov 20, 2025

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

2.3K
Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells
08:38

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells

Published on: March 3, 2015

13.7K
Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA
10:21

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Published on: February 23, 2024

3.3K

Area of Science:

  • Structural biology
  • Computational biology
  • Bioinformatics

Background:

  • Understanding protein-protein interaction (PPI) interfaces is crucial for elucidating molecular functions, disease mechanisms, and identifying therapeutic targets.
  • Experimental determination of protein complex structures is time-consuming, necessitating computational approaches for structural insights.
  • Current molecular docking methods often struggle to accurately identify native-like PPI interfaces based on scoring functions alone.

Purpose of the Study:

  • To investigate and identify distinct structural features that differentiate native protein-protein complex interfaces from non-native ones.
  • To develop a computational model for classifying protein-protein complexes as native-like or non-native.
  • To provide a web server tool for predicting the quality of protein-protein interfaces.

Main Methods:

  • In-depth analysis of structural properties of known native and non-native protein-protein interfaces (homo- and hetero-complexes).
  • Development and implementation of a support vector machine (SVM) based classification scheme using identified interface properties.
  • Generation of 3D models for experimentally validated but structurally unresolved protein interactions to predict interfaces.

Main Results:

  • Identification of statistically significant differences in interface properties between native and non-native protein-protein complexes.
  • Demonstration of high performance for the SVM-based classification scheme in distinguishing native-like interfaces from docking decoys.
  • Successful prediction of likely interfaces for protein interactions lacking experimental structural data.

Conclusions:

  • Interface properties can effectively distinguish native from non-native protein-protein complexes, overcoming limitations of traditional docking scores.
  • The developed SVM model offers a robust computational approach for assessing the quality of predicted protein-protein interfaces.
  • The PCPIP web server provides a valuable resource for researchers to predict and evaluate protein-protein interfaces, aiding in drug discovery and biological pathway analysis.