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 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,...

Peptide Identification Using Tandem Mass Spectrometry

Peptide Identification Using Tandem Mass Spectrometry

Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...

You might also read

Related Articles

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

Sort by

Same author

Computer-aided design, molecular dynamics simulations and in-vitro inhibitory potential of piperazine bridged bis-thiadiazole benzothioate derivatives against platelet-derived endothelial cell growth factor.

Journal of computer-aided molecular design·2026

Same author

Harnessing angular geometry in deep learning for protein-ligand binding affinity prediction.

Computer methods and programs in biomedicine·2026

Same author

Efficient drug-target affinity prediction via interaction features and parallel CNN-BiLSTM with attention.

Computational biology and chemistry·2026

Same author

Advances in visible and ultraviolet self-powered photodetectors: exploring 2D materials and Janus heterostructures.

Nanoscale·2025

Same author

Predisposition of an Intronic Duplication in CHEK2 Gene in the Cases of Breast Cancer from Balochistan.

Asian Pacific journal of cancer prevention : APJCP·2025

Same author

Irreducible Dislocation of the Great Toe Interphalangeal Joint Secondary to an Incarcerated Sesamoid: A Retrospective Case Series of Six Patients.

Journal of orthopaedic case reports·2025

Search research articles

Related Experiment Video

Updated: Jul 9, 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

PepCNN deep learning tool for predicting peptide binding residues in proteins using sequence, structural, and

Abel Chandra¹, Alok Sharma^2,3,4, Iman Dehzangi^5,6

¹Institute for Integrated and Intelligent Systems, Griffith University, Brisbane, Australia. abel.chandra@griffithuni.edu.au.

Scientific Reports

|November 28, 2023

Summary

This summary is machine-generated.

We developed PepCNN, a deep learning model for predicting protein-peptide interactions. PepCNN improves accuracy using protein structure and sequence data, aiding drug discovery and understanding cellular processes.

More Related Videos

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: 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

Related Experiment Videos

Last Updated: Jul 9, 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

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: 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

Area of Science:

Biochemistry
Computational Biology
Genomics

Background:

Protein-peptide interactions are fundamental to cellular functions and disease development, including cancer.
Current experimental methods for studying these interactions are resource-intensive.
Computational prediction methods often lack sufficient accuracy.

Purpose of the Study:

To develop an accurate computational model for predicting protein-peptide interactions.
To leverage deep learning and integrate diverse biological data for enhanced prediction.
To provide a valuable tool for functional genomics and drug discovery.

Main Methods:

Introduced PepCNN, a deep learning model utilizing primary protein sequence information.
Incorporated structural features like half-sphere exposure.
Integrated position-specific scoring matrices and pre-trained protein language model embeddings.

Main Results:

PepCNN demonstrated superior performance compared to existing state-of-the-art methods.
Achieved high specificity, precision, and Area Under the Curve (AUC).
The model effectively combines sequence and structural data for accurate predictions.

Conclusions:

PepCNN offers a significant advancement in predicting protein-peptide interactions.
The model's accuracy supports its utility in functional genomics and drug discovery.
Publicly available software and datasets facilitate further research and application.