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Related Concept Videos

Protein Kinases and Phosphatases02:54

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 Phosphatases02:54

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...
Phosphorylation01:02

Phosphorylation

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...
Phosphorylation01:02

Phosphorylation

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...
Conserved Binding Sites01:49

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 analyses the...

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Related Experiment Video

Updated: May 12, 2026

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

Data construction for phosphorylation site prediction.

Haipeng Gong, Xiaoqing Liu, Jun Wu

    Briefings in Bioinformatics
    |April 2, 2013
    PubMed
    Summary
    This summary is machine-generated.

    Evaluating computational protein phosphorylation site prediction requires careful data construction. Different methods significantly impact performance, highlighting the need to choose unbiased test data and training methods for specific real-world scenarios.

    Keywords:
    Friedman testWilcoxon signed-ranks testclassificationgeneralization performancephosphorylation site prediction

    More Related Videos

    Oligopeptide Competition Assay for Phosphorylation Site Determination
    09:16

    Oligopeptide Competition Assay for Phosphorylation Site Determination

    Published on: May 18, 2017

    Related Experiment Videos

    Last Updated: May 12, 2026

    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

    Oligopeptide Competition Assay for Phosphorylation Site Determination
    09:16

    Oligopeptide Competition Assay for Phosphorylation Site Determination

    Published on: May 18, 2017

    Area of Science:

    • Molecular Biology
    • Bioinformatics

    Background:

    • Protein phosphorylation is a key post-translational modification regulating cellular processes.
    • Experimental identification of phosphorylation sites via mass spectrometry is resource-intensive.
    • Computational methods for phosphorylation site prediction are crucial but require robust evaluation.

    Purpose of the Study:

    • To categorize existing data construction methods for phosphorylation site prediction.
    • To assess the impact of different data construction methods on algorithm evaluation.
    • To identify unbiased test data sets and optimal training data strategies for diverse scenarios.

    Main Methods:

    • Categorization of existing training and test data construction methods.
    • Comprehensive experimental studies for non-kinase-specific and kinase-specific prediction tasks.
    • Comparative analysis of prediction performance across different data construction strategies.

    Main Results:

    • Data construction methods significantly influence prediction performance.
    • Unbiased test data sets vary depending on real-world application scenarios.
    • Different training data construction methods exhibit varying generalization capabilities.

    Conclusions:

    • The choice of data construction methods is critical for accurate phosphorylation site prediction algorithm assessment.
    • Future research should focus on scenario-specific evaluation using appropriate unbiased test data.
    • Selecting training data construction methods with superior generalization performance is essential for broader applicability.