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Related Concept Videos

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...
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

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Protein kinases
Many proteins in the cell are regulated by phosphorylation, the addition of a phosphate group. A family of enzymes called kinases...
Protein Networks02:26

Protein Networks

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,...
Protein Networks02:26

Protein Networks

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.
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Protein-protein Interfaces

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Related Experiment Video

Updated: Jun 18, 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

A structural informatics approach to mine kinase knowledge bases.

Natasja Brooijmans1, Dominick Mobilio, Gary Walker

  • 1Computational Chemistry and Cheminformatics, Wyeth Research, 401 North Middletown Road, Pearl River, NY 10965, USA.

Drug Discovery Today
|December 2, 2009
PubMed
Summary

This study introduces novel structural informatics methods to analyze kinase ATP-binding sites using existing databases. The approach focuses on ligand-bound geometries and structure-activity relationship data for Abelson kinase inhibitors.

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Characterization at the Molecular Level using Robust Biochemical Approaches of a New Kinase Protein
11:23

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

Published on: June 30, 2019

Related Experiment Videos

Last Updated: Jun 18, 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

Characterization at the Molecular Level using Robust Biochemical Approaches of a New Kinase Protein
11:23

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

Published on: June 30, 2019

Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Chemistry

Background:

  • Kinase ATP-binding sites are crucial drug targets.
  • Existing methods for analyzing protein structures have limitations.
  • Databases like the Protein Data Bank contain valuable structural information.

Purpose of the Study:

  • To develop and describe novel structural informatics approaches.
  • To focus on mining kinase ATP-binding site data.
  • To create a system centered on ligand-bound geometries and SAR data.

Main Methods:

  • Utilizing structural informatics techniques.
  • Mining data from the Protein Data Bank and GVK database.
  • Creating a database of ligand-bound geometries relative to binding site residues.
  • Integrating ligand-based structure-activity relationship (SAR) data.

Main Results:

  • Demonstrated a novel approach for analyzing kinase ATP-binding sites.
  • Developed a system focused on ligand-bound geometries and SAR data.
  • Successfully illustrated the system's utility with Abelson kinase and related inhibitors.

Conclusions:

  • The described structural informatics combination offers a new perspective on analyzing kinase ATP-binding sites.
  • The focus on ligand-bound geometries and SAR data provides valuable insights for drug discovery.
  • The system is effective for studying specific kinase families and their inhibitors.