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...

You might also read

Related Articles

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

Sort by

Same author

LIG1 Loss in TP53-mutant Triple Negative Breast Cancer Rewires DNA Repair and Confers Sensitivity to PARP-ATR Inhibitor Combinations.

Molecular cancer therapeutics·2026

Same author

A data-driven framework reconstructs the molecular continuum of human MASLD progression.

Nature metabolism·2026

Same author

TROP2 targeting reveals therapy-driven cell state dynamics in colorectal cancer.

Nature·2026

Same author

From knowledge graph to topological data analysis: a novel framework to analyze gene regulatory networks for tomato-multi-pathogen interactions.

The New phytologist·2026

Same author

ParTIpy: a scalable framework for archetypal analysis and Pareto task inference.

Molecular systems biology·2026

Same author

Integrated proteogenomic and metabolomic profiling of acute myeloid leukemias to identify molecular subtypes and associated therapy targets.

Nature cancer·2026

Search research articles

Related Experiment Video

Updated: Sep 20, 2025

Characterization at the Molecular Level using Robust Biochemical Approaches of a New Kinase Protein

Characterization at the Molecular Level using Robust Biochemical Approaches of a New Kinase Protein

Published on: June 30, 2019

Comprehensive evaluation of phosphoproteomic-based kinase activity inference.

Sophia Müller-Dott¹, Eric J Jaehnig², Khoi Pham Munchic³

¹Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany.

Nature Communications

|May 22, 2025

Summary

benchmarKIN, an R package, evaluates kinase activity inference methods using phosphoproteomics data. Manually curated libraries and predicted kinase-substrate interactions improve accuracy in identifying deregulated kinases for disease research.

More Related Videos

Identification of Kinase-substrate Pairs Using High Throughput Screening

Identification of Kinase-substrate Pairs Using High Throughput Screening

Published on: August 29, 2015

Assaying Protein Kinase Activity with Radiolabeled ATP

Assaying Protein Kinase Activity with Radiolabeled ATP

Published on: May 26, 2017

Related Experiment Videos

Last Updated: Sep 20, 2025

Characterization at the Molecular Level using Robust Biochemical Approaches of a New Kinase Protein

Characterization at the Molecular Level using Robust Biochemical Approaches of a New Kinase Protein

Published on: June 30, 2019

Identification of Kinase-substrate Pairs Using High Throughput Screening

Identification of Kinase-substrate Pairs Using High Throughput Screening

Published on: August 29, 2015

Assaying Protein Kinase Activity with Radiolabeled ATP

Assaying Protein Kinase Activity with Radiolabeled ATP

Published on: May 26, 2017

Area of Science:

Molecular Biology
Bioinformatics
Systems Biology

Background:

Kinases are crucial regulators of cellular processes, implicated in numerous diseases.
Inferring kinase activity from phosphoproteomics data is vital but limited by current methods and kinase-substrate libraries.
Existing inference methods yield variable results, requiring robust evaluation for reliable interpretation.

Purpose of the Study:

To introduce benchmarKIN, an R package for comprehensive evaluation of kinase activity inference methods.
To benchmark kinase-substrate libraries, inference algorithms, and the utility of predicted interactions.
To demonstrate the application of kinase activity inference in characterizing kinase inhibitor responses.

Main Methods:

Development of benchmarKIN, an R package for evaluating kinase activity inference.
Utilized classical perturbation experiments and a novel tumor-based benchmarking approach with multi-omics data.
Evaluated kinase-substrate libraries, inference algorithms, and incorporated predicted kinase-substrate interactions (NetworKIN).

Main Results:

Most computational inference methods performed similarly; however, library choice significantly impacted inferred kinase activities.
Manually curated kinase-substrate libraries demonstrated superior performance in recapitulating known kinase activities.
Integrating predicted targets from NetworKIN further enhanced performance in tumor-based evaluations.

Conclusions:

benchmarKIN provides a robust framework for evaluating kinase activity inference methods.
The selection of high-quality, manually curated kinase-substrate libraries is critical for accurate kinase activity inference.
benchmarKIN aids researchers in selecting reliable methods for identifying deregulated kinases and understanding kinase inhibitor responses.