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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...
Receptor Tyrosine Kinases01:26

Receptor Tyrosine Kinases

Receptor tyrosine kinases or RTKs are membrane-bound receptors that phosphorylate specific tyrosine on protein substrates. RTKs regulate cellular growth, differentiation, survival, and migration. They contain an extracellular ligand binding domain, a transmembrane domain, and a cytosolic tail with intrinsic kinase activity. Several extracellular signaling molecules activate RTKs in one or more ways and relay the signal downstream. Ligands such as platelet-derived growth factor (PDGF) or...
MAPK Signaling Cascades01:07

MAPK Signaling Cascades

Mitogen-activated protein kinase, or MAPK pathway, activates three sequential kinases to regulate cellular responses such as proliferation, differentiation, survival, and apoptosis. The canonical MAPK pathway starts with a mitogen or growth factor binding to an RTK. The activated RTKs stimulate Ras, which recruits Raf or MAP3 Kinase (MAPKKK), the first kinase of the MAPK signaling cascade. Raf further phosphorylates and activates MEK or MAP2 Kinases (MAPKK), which in turn phosphorylates MAP...
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: Jun 28, 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

Prediction of kinase-specific phosphorylation sites using conditional random fields.

Thanh Hai Dang1, Koenraad Van Leemput, Alain Verschoren

  • 1Intelligent Systems Laboratory and Advanced Database Research and Modelling, Department of Mathematics and Computer Science, Middelheimlaan 1, B-2020 Antwerpen, Belgium.

Bioinformatics (Oxford, England)
|October 23, 2008
PubMed
Summary

This study introduces a new computational method using conditional random fields (CRFs) to accurately predict protein phosphorylation sites. The CRPhos tool offers improved performance over existing methods for kinase-specific phosphorylation site prediction.

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Related Experiment Videos

Last Updated: Jun 28, 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

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

Area of Science:

  • Biochemistry
  • Bioinformatics
  • Computational Biology

Background:

  • Phosphorylation is a key post-translational modification regulating biological processes.
  • Kinases catalyze phosphorylation, recognizing specific substrate sites.
  • Existing computational models for predicting phosphorylation sites have limitations in capturing sequence dependencies.

Purpose of the Study:

  • To develop a novel computational approach for predicting protein phosphorylation sites.
  • To address limitations of existing models by considering amino acid dependencies.

Main Methods:

  • Utilized a conditional random field (CRF) model trained on a positive dataset of phosphorylation sites.
  • Employed a negative training dataset to define a decision threshold for a specific false positive rate.
  • Implemented the method in a tool called CRPhos.

Main Results:

  • The proposed CRF-based method demonstrates strong performance on benchmark phosphorylation data (Phospho.ELM).
  • CRPhos generally outperforms existing methods for predicting phosphorylation sites across various kinases.
  • This represents the first application of CRFs for predicting post-translational modification sites.

Conclusions:

  • Conditional random fields offer a powerful approach for accurate phosphorylation site prediction.
  • The CRPhos tool provides a valuable resource for researchers studying protein phosphorylation.
  • This work advances the field of computational prediction of post-translational modifications.