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

13.3K
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...
13.3K
Phosphorylation01:02

Phosphorylation

50.8K
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...
50.8K
Conserved Binding Sites01:49

Conserved Binding Sites

4.3K
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...
4.3K
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

88
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
88

You might also read

Related Articles

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

Sort by
Same author

Observation of tunable chiral spin textures with nonlinear optics.

Nature communications·2026
Same author

FSCL-BC: Federated supervised contrastive learning for breast cancer diagnosis with high sensitivity.

Computer methods and programs in biomedicine·2026
Same author

Segmentation and classification of hippocampal subregions using multi-task generative adversarial networks.

Scientific reports·2026
Same author

Deep learning multi-omics integration identifies new molecular subtypes of lung cancer.

BioData mining·2026
Same author

ExPO: an exposure-conditioned neural operator for L1000 signature prediction.

Journal of cheminformatics·2026
Same author

Evolving mortality trends in hypertension-associated ischemic heart disease among U.S. adults over two decades: a CDC wonder analysis (2000-2023).

Journal of human hypertension·2026
Same journal

Hierarchical analysis of metabolic phenotype reveals distinct microbiota and circulatory transcriptome in metabolic dysfunction-associated steatotic liver disease.

Gene·2026
Same journal

Mutation T71R enhanced the structural stability and functional activity of wild type superoxide dismutase cloned from soil metagenome.

Gene·2026
Same journal

Reduced ATXN1 expression as an adverse prognostic indicator in Acute myeloid leukemia.

Gene·2026
Same journal

Constructing regulatory networks of Rubisco post-translational modifications: a novel avenue for engineering environment adaptive plants.

Gene·2026
Same journal

Traumatic brain injury enhances fracture healing by upregulating VNN1 to activate the Wnt/β-catenin signaling pathway.

Gene·2026
Same journal

Single-cell transcriptomics reveals CCL2-mediated macrophage-endothelial cell interactions drive apoptosis in varicose veins.

Gene·2026
See all related articles

Related Experiment Video

Updated: Aug 24, 2025

Oligopeptide Competition Assay for Phosphorylation Site Determination
09:16

Oligopeptide Competition Assay for Phosphorylation Site Determination

Published on: May 18, 2017

8.5K

Accurately predicting microbial phosphorylation sites using evolutionary and structural features.

Faisal Ahmed1, Iman Dehzangi2, Md Mehedi Hasan3

  • 1Department of Computer Science and Engineering, United International University, Dhaka, Bangladesh; Department of Computer Science and Engineering, Premier University, Chattogram, Bangladesh.

Gene
|October 22, 2022
PubMed
Summary
This summary is machine-generated.

This study introduces RotPhoPred, a novel computational tool for predicting microbial phosphorylation sites (pS, pT, pY). RotPhoPred integrates evolutionary and structural data, offering a faster, more accurate alternative to experimental methods for understanding host-pathogen interactions.

Keywords:
ClassificationEvolutionary featuresMachine learningPhosphorylationPost translational modificationStructural features

More Related Videos

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins
09:40

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Published on: June 11, 2015

12.3K
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

18.8K

Related Experiment Videos

Last Updated: Aug 24, 2025

Oligopeptide Competition Assay for Phosphorylation Site Determination
09:16

Oligopeptide Competition Assay for Phosphorylation Site Determination

Published on: May 18, 2017

8.5K
Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins
09:40

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Published on: June 11, 2015

12.3K
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

18.8K

Area of Science:

  • Biochemistry
  • Bioinformatics
  • Computational Biology

Background:

  • Post-translational modifications (PTMs) are crucial for protein function.
  • Phosphorylation, a key PTM, regulates vital cellular processes like communication and gene regulation.
  • Predicting microbial phosphorylation sites aids in understanding host-pathogen interactions and developing antimicrobials, but experimental methods are costly and time-consuming.

Purpose of the Study:

  • To develop an accurate and efficient computational method for predicting microbial phosphorylation sites.
  • To introduce RotPhoPred, a novel predictor for phospho-serine (pS), phospho-threonine (pT), and phospho-tyrosine (pY) sites.

Main Methods:

  • Integration of evolutionary bigram profiles with structural information.
  • Utilizing Rotation Forest as the classification algorithm.
  • Development of RotPhoPred, a novel approach for predicting microbial phosphorylation sites.

Main Results:

  • RotPhoPred achieved high performance metrics: sensitivity (90.0% for pS, 75.4% for pT, 78.2% for pY), specificity (92.1% for pS, 97.2% for pT, 94.7% for pY), and accuracy (91.0% for pS, 86.3% for pT, 86.4% for pY).
  • The study highlights the novelty of the extracted features and the employed classifier for this specific task.
  • Comparative analysis demonstrated RotPhoPred's superiority over existing methods.

Conclusions:

  • RotPhoPred offers a significant advancement in predicting microbial phosphorylation sites.
  • The tool provides a valuable, cost-effective alternative to experimental prediction methods.
  • RotPhoPred is publicly available, facilitating further research in microbial pathogenesis and drug development.