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 Kinases and Phosphatases

Protein Kinases and Phosphatases

Proteins undergo chemical modifications that trigger changes in the charge, structure, and conformation of the proteins. Phosphorylation, acetylation, glycosylation, nitrosylation, ubiquitination, lipidation, methylation, and proteolysis are various protein modifications that regulate protein activity. Such modifications are usually enzyme-driven.
Protein kinases
Many proteins in the cell are regulated by phosphorylation, the addition of a phosphate group. A family of enzymes called kinases...

Protein Kinases and Phosphatases

Protein Kinases and Phosphatases

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

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...

Factors Affecting Protein-Drug Binding: Drug Interactions

Factors Affecting Protein-Drug Binding: Drug Interactions

Drug interactions are a critical aspect of pharmacology and can occur when two or more drugs compete for the same binding site. This competition can result in one drug displacing another, altering the effect of the displaced drug. Drug interactions are complex processes that rely heavily on how much of the displacer drug is present and how strongly it can bind to the same sites as the displaced drug.
Displacement interactions can have varying outcomes, ranging from toxicity to virtually...

You might also read

Related Articles

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

Sort by

Same author

SACall: A Neural Network Basecaller for Oxford Nanopore Sequencing Data Based on Self-Attention Mechanism.

IEEE/ACM transactions on computational biology and bioinformatics·2020

Same author

Identification of early mild cognitive impairment using multi-modal data and graph convolutional networks.

BMC bioinformatics·2020

Same author

DeepFrag-k: a fragment-based deep learning approach for protein fold recognition.

BMC bioinformatics·2020

Same author

Predicting unrecognized enhancer-mediated genome topology by an ensemble machine learning model.

Genome research·2020

Same author

Drug-drug similarity measure and its applications.

Briefings in bioinformatics·2020

Same author

Computational drug repositioning based on multi-similarities bilinear matrix factorization.

Briefings in bioinformatics·2020

Search research articles

Related Experiment Video

Updated: Jan 26, 2026

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Published on: November 18, 2014

Identifying Interactions Between Kinases and Substrates Based on Protein-Protein Interaction Network.

Qingfeng Chen^1,2, Canshang Deng¹, Wei Lan¹

¹1School of Computer, Electronics and Information, Guangxi University, Nanning, China.

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology

|April 17, 2019

Summary

This study introduces a novel computational method for predicting kinase-substrate interactions using protein-protein interaction networks. The new approach enhances accuracy by leveraging network topology and clustering for more reliable similarity measures.

Keywords:

bi-random walk kinase–substrate interaction protein phosphorylation protein–protein interaction network

More Related Videos

TurboID-Based Proximity Labeling for In Planta Identification of Protein-Protein Interaction Networks

TurboID-Based Proximity Labeling for In Planta Identification of Protein-Protein Interaction Networks

Published on: May 17, 2020

Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation

Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation

Published on: August 21, 2019

Related Experiment Videos

Last Updated: Jan 26, 2026

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Published on: November 18, 2014

TurboID-Based Proximity Labeling for In Planta Identification of Protein-Protein Interaction Networks

TurboID-Based Proximity Labeling for In Planta Identification of Protein-Protein Interaction Networks

Published on: May 17, 2020

Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation

Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation

Published on: August 21, 2019

Area of Science:

Biochemistry
Computational Biology
Systems Biology

Background:

Protein phosphorylation is a crucial post-translational modification in eukaryotes, regulating numerous biological processes.
Understanding kinase-substrate interactions is vital for elucidating disease mechanisms.
Existing computational methods often rely heavily on local protein sequence information.

Purpose of the Study:

To develop a novel computational method for predicting kinase-substrate interactions.
To utilize protein-protein interaction (PPI) networks for improved prediction accuracy.
To address limitations of existing methods focused on local sequence information.

Main Methods:

Constructing and analyzing protein-protein interaction (PPI) networks.
Measuring kinase-kinase and substrate-substrate similarities within the PPI network.
Adjusting similarity measures based on cluster membership for enhanced reliability.
Employing a bi-random walk algorithm for predicting potential kinase-substrate interactions.

Main Results:

The proposed method demonstrates superior performance compared to state-of-the-art algorithms.
Experimental results validate the effectiveness of the PPI network-based approach.
A case study confirmed the method's capability in identifying potential kinase-substrate interactions.

Conclusions:

The novel computational method effectively predicts kinase-substrate interactions by integrating PPI network information.
Leveraging network topology and clustering improves the reliability of similarity assessments.
This approach offers a promising tool for biological research and disease mechanism studies.