Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Protein Kinases and Phosphatases02:54

Protein Kinases and Phosphatases

12.1K
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...
12.1K
Protein Kinases and Phosphatases02:54

Protein Kinases and Phosphatases

3.3K
3.3K
Phosphorylation01:02

Phosphorylation

44.8K
The addition or removal of phosphate groups from proteins is the most common chemical modification that regulates cellular processes. These modifications can affect the structure, activity, stability, and localization of proteins within cells as well as their interactions with other proteins.
During phosphorylation, protein kinases transfer the terminal phosphate group of ATP to specific amino acid side chains of substrate proteins. Serine, threonine, and tyrosine are the most commonly...
44.8K
Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

8.2K
Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein....
8.2K
Phosphoinositides and PIPs01:42

Phosphoinositides and PIPs

7.7K
Phosphoinositides are a group of phospholipids containing a glycerol backbone with two fatty acid chains and a phosphate attached to a myoinositol sugar ring. The inositol head group extends into the cytoplasm, where it is modified by adding phosphate groups to form phosphatidylinositol phosphates or PIPs.
Different phosphoinositides are synthesized and recruited on the cytosolic face of the plasma membrane. The localization of specific phosphoinositides concentrated in separate membrane...
7.7K
Protein Networks02:26

Protein Networks

3.7K
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,...
3.7K

You might also read

Related Articles

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

Sort by
Same author

Genome-wide DNA methylation dynamics and RNA-seq analysis during grape (cv. 'Cabernet Franc') skin coloration.

GenomicsĀ·2024
Same author

Delivery Strategies for Colchicine as a Critical Dose Drug: Reducing Toxicity and Enhancing Efficacy.

PharmaceuticsĀ·2024
Same author

Occult urothelial carcinoma with mediastinal metastasis: A case report.

Oncology lettersĀ·2024
Same author

Phase Identification and Discovery of an Elusive Polymorph of Drug-Polymer Inclusion Complex Using Automated 3D Electron Diffraction.

Angewandte Chemie (International ed. in English)Ā·2024
Same author

Mediating and moderating effects of authoritative parenting styles on adolescent behavioral problems.

Frontiers in psychologyĀ·2024
Same author

A transformer-based diffusion probabilistic model for heart rate and blood pressure forecasting in Intensive Care Unit.

Computer methods and programs in biomedicineĀ·2024

Related Experiment Video

Updated: May 3, 2026

Identification of Kinase-substrate Pairs Using High Throughput Screening
11:13

Identification of Kinase-substrate Pairs Using High Throughput Screening

Published on: August 29, 2015

7.8K

Literature mining of protein phosphorylation using dependency parse trees.

Mang Wang1, Hong Xia1, Dongdong Sun1

  • 1School of Information Science and Technology, University of Science and Technology of China, Hefei AH230027, China.

Methods (San Diego, Calif.)
|January 21, 2014
PubMed
Summary

This study introduces a novel text-mining method to automatically extract protein phosphorylation information from scientific literature. The approach significantly improves the retrieval of substrates, kinases, and phosphorylation sites, aiding drug design and disease research.

Keywords:
Dependency parse treePhosphorylationSystems biologyText mining

More Related Videos

A Mass Spectrometry-Based Approach to Identify Phosphoprotein Phosphatases and their Interactors
10:17

A Mass Spectrometry-Based Approach to Identify Phosphoprotein Phosphatases and their Interactors

Published on: April 29, 2022

1.8K
Identification of Cyclin-dependent Kinase 1 Specific Phosphorylation Sites by an In Vitro Kinase Assay
12:26

Identification of Cyclin-dependent Kinase 1 Specific Phosphorylation Sites by an In Vitro Kinase Assay

Published on: May 3, 2018

18.3K

Related Experiment Videos

Last Updated: May 3, 2026

Identification of Kinase-substrate Pairs Using High Throughput Screening
11:13

Identification of Kinase-substrate Pairs Using High Throughput Screening

Published on: August 29, 2015

7.8K
A Mass Spectrometry-Based Approach to Identify Phosphoprotein Phosphatases and their Interactors
10:17

A Mass Spectrometry-Based Approach to Identify Phosphoprotein Phosphatases and their Interactors

Published on: April 29, 2022

1.8K
Identification of Cyclin-dependent Kinase 1 Specific Phosphorylation Sites by an In Vitro Kinase Assay
12:26

Identification of Cyclin-dependent Kinase 1 Specific Phosphorylation Sites by an In Vitro Kinase Assay

Published on: May 3, 2018

18.3K

Area of Science:

  • Biochemistry
  • Bioinformatics
  • Computational Biology

Background:

  • Protein phosphorylation is a common post-translational modification crucial for biological processes.
  • Extracting phosphorylation data from biomedical literature is challenging due to information volume and complex expression.
  • Accurate phosphorylation information is vital for understanding molecular mechanisms, disease treatment, and drug design.

Purpose of the Study:

  • To develop an automated text-mining method for efficient retrieval of protein phosphorylation information.
  • To overcome the challenges associated with extracting phosphorylation data from large-scale biomedical literature.

Main Methods:

  • Utilized natural language processing (NLP) techniques.
  • Transformed sentences into dependency parse trees to capture relationships between keywords.
  • Extracted substrate, kinase, and phosphorylation site information using syntactic patterns.

Main Results:

  • The proposed method demonstrated significantly improved performance compared to existing approaches.
  • Successfully retrieved detailed protein phosphorylation information, including substrates, kinases, and sites.
  • Developed a web server for public access to the tool.

Conclusions:

  • The novel text-mining method offers a powerful bioinformatics approach for extracting phosphorylation data.
  • The method enhances the ability to mine biomedical literature for critical phosphorylation insights.
  • The freely available web server facilitates broader research applications.