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...

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...

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 Organization

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....

You might also read

Related Articles

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

Sort by

Same author

The role and therapeutic potential of nanotechnology-mediated ferroptosis regulation in myelodysplastic syndromes.

Frontiers in oncology·2026

Same author

Correction to "From Solubilization to Structural Perturbation: The Mechanism of Polyquaternium-51-Driven Enhanced Transdermal Delivery of Glabridin".

Langmuir : the ACS journal of surfaces and colloids·2026

Same author

A Six-Year Longitudinal Cohort Study Assessing the Association Between Social Interaction Trajectories and Sleep Health in Older Adults.

Journal of visualized experiments : JoVE·2026

Same author

Microbe-arsenic interactions in groundwater: From community evolution to functional regulation.

Ecotoxicology and environmental safety·2026

Same author

Development and Application of a Blocking ELISA for the Detection of Feline Calicivirus Antibodies Based on Monoclonal Antibodies Against VP1 Protein.

Transboundary and emerging diseases·2026

Same author

From Solubilization to Structural Perturbation: The Mechanism of Polyquaternium-51-Driven Enhanced Transdermal Delivery of Glabridin.

Langmuir : the ACS journal of surfaces and colloids·2026

Search research articles

Related Experiment Video

Updated: Jun 7, 2025

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

ProBID-Net: a deep learning model for protein-protein binding interface design.

Zhihang Chen¹, Menglin Ji¹, Jie Qian¹

¹Department of Medicinal Chemistry, School of Pharmacy, Fudan University 826 Zhangheng Road Shanghai 201203 People's Republic of China wangrx@fudan.edu.cn yfqi@fudan.edu.cn.

Chemical Science

|November 21, 2024

Summary

ProBID-Net is a new AI tool that designs specific binding proteins by learning from known protein structures. It excels at protein-protein interaction design, even predicting mutation effects without prior training data.

More Related Videos

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

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

Published on: February 23, 2024

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Related Experiment Videos

Last Updated: Jun 7, 2025

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

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

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

Published on: February 23, 2024

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Area of Science:

Computational biology
Protein engineering
Artificial intelligence in drug discovery

Background:

Protein-protein interactions (PPIs) are fundamental to biological processes.
Computational design of PPIs is vital for biopharmaceutical development.
Current AI models often struggle with designing interactions for known receptor sequences.

Purpose of the Study:

To introduce ProBID-Net, an AI model for designing specific binding proteins based on known target structures.
To address the limitations of existing AI models in protein-protein interaction design.
To enable the creation of novel binding proteins for biopharmaceutical applications.

Main Methods:

ProBID-Net was trained on natural protein-protein complex and domain-interface structures.
The model identifies features from known protein structures to design binding proteins.
Performance was evaluated using interface sequence recovery rates and AlphaFold-Multimer validation.

Main Results:

ProBID-Net achieved high interface sequence recovery rates (52.7%, 43.9%, 37.6%), matching or exceeding ProteinMPNN.
Sequences designed by ProBID-Net showed strong correlation between design targets and predicted structures (AlphaFold-Multimer).
The model demonstrated zero-shot prediction capabilities for binding affinity changes upon mutation.

Conclusions:

ProBID-Net advances computational protein design for specific protein-protein interactions.
The model offers a powerful tool for creating novel binding proteins.
ProBID-Net has significant potential for biopharmaceutical research and development.