Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Protein-protein Interfaces

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...

Protein-Protein Interfaces

Protein-Protein Interfaces

Protein Networks

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,...

Protein Networks

Protein Networks

Conserved Binding Sites

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...

Ligand Binding Sites

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...

You might also read

Related Articles

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

Sort by

Same author

Nerol as an anti-quorum sensing and therapeutic agent against <i>Acinetobacter baumannii</i> pneumonia.

iScience·2026

Same author

Cancer-Associated Adipocytes in Human Breast Cancer: An Observational Histopathological Study of Dedifferentiation and Stromal Transition.

The breast journal·2026

Same author

Synergistic Growth and Metabolic Interactions of <i>Kluyveromyces marxianus</i> and <i>Lactococcus lactis</i> in Rose-Aroma Fermented Milk Revealed by Integrated Flavoromics and Metabolomics.

Metabolites·2026

Same author

Tertiary alcohol-containing polycyclic polyprenylated acylphloroglucinols from Hypericum scabrum inhibit the proliferation of oral squamous cell carcinoma CAL-27 cells.

Scientific reports·2026

Same author

Silicone Rubber Triboelectric Nanogenerator for Self-Powered Wide-Range Frequency Vibration Monitoring.

Nanomaterials (Basel, Switzerland)·2026

Same author

Co-assembled quercetin-proanthocyanidin nanoparticles for improved stability and flavor properties.

Food research international (Ottawa, Ont.)·2026

Same journal

Isolation of Mesenchymal Stem Cell-Derived Extracellular Vesicles.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Modeling Melanoma Immune Surveillance by CAR-T Cells in Human Skin Organoids.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Stepwise Optimization of a Matrigel-Based In Vitro Angiogenesis Assay for Reproducible and Quantifiable 2D-Tube Formation Using HUVECs.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Quantifying Mechanical Properties of Fresh Ovarian Tissue with Optical Brillouin Microscopy.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

3D Chromatin Architecture During Early Development: New Methods and New Findings.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Metabolic Plasticity in Embryogenesis Throughout the Lens of NAD<sup></sup>.

Methods in molecular biology (Clifton, N.J.)·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jan 6, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

A Web-Based Protocol for Interprotein Contact Prediction by Deep Learning.

Xiaoyang Jing^1,2, Hong Zeng³, Sheng Wang¹

¹Toyota Technological Institute at Chicago, Chicago, IL, USA.

Methods in Molecular Biology (Clifton, N.J.)

|October 5, 2019

Summary

This summary is machine-generated.

Predicting protein-protein contacts is vital for cell function. RaptorX-ComplexContact, a new deep learning web server, accurately identifies these contacts using paired protein sequence alignments and neural networks.

Keywords:

Deep learning (DL)Direct-coupling analysis (DCA)Interprotein contact prediction Multiple sequence alignment (MSA)Protein complex Protein docking Protein interaction network Protein–protein interaction (PPI) prediction

More Related Videos

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

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

Published on: January 26, 2024

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Related Experiment Videos

Last Updated: Jan 6, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

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

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

Published on: January 26, 2024

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Area of Science:

Biochemistry and Molecular Biology
Computational Biology
Bioinformatics

Background:

Accurate identification of residue-residue contacts in protein-protein interactions is essential for understanding protein function and cellular mechanisms.
Existing methods like direct-coupling analysis (DCA) require numerous sequence homologs for reliable predictions, limiting their applicability.

Purpose of the Study:

To develop an advanced computational tool for predicting interprotein residue-residue contacts.
To leverage deep learning for improved accuracy in contact prediction compared to traditional methods.

Main Methods:

Developed RaptorX-ComplexContact, a web server utilizing deep convolutional residual neural networks (ResNet).
Constructed paired multiple sequence alignments (MSAs) using genomic distance and phylogenetic information from sequence homologs.
Integrated sequential features and coevolutionary information from paired MSAs for contact prediction.

Main Results:

RaptorX-ComplexContact demonstrates effective prediction of interprotein residue-residue contacts.
The method utilizes deep learning architectures for enhanced prediction accuracy.

Conclusions:

RaptorX-ComplexContact provides a valuable resource for predicting interprotein contacts.
This tool can significantly aid in protein docking, protein-protein interaction prediction, and the construction of protein interaction networks.