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Updated: Jun 20, 2026
07:28
JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
Published on: October 19, 2021
Network and pathway analysis of compound-protein interactions
Richard J Brennan1, Tatiana Nikolskya, Svetlana Bureeva
1GeneGo Inc., Encinitas, CA, USA.
Methods in Molecular Biology (Clifton, N.J.)
|September 4, 2009
Summary
This study presents an integrated computational system for predicting xenobiotic effects on biological systems. It aids in early compound evaluation, prioritizing drug candidates and guiding medicinal chemistry efforts.
Area of Science:
- Computational toxicology
- Systems biology
- Cheminformatics
Background:
- Evaluating xenobiotic effects is crucial for drug discovery and safety.
- Existing methods often lack integrated approaches for comprehensive in silico assessment.
Purpose of the Study:
- To develop and demonstrate an integrated computational system for in silico evaluation of xenobiotic effects.
- To enable early prioritization of compounds and guide medicinal chemistry.
Main Methods:
- Integration of predictive chemical analyses, chemogenomics knowledge bases, and systems biology network reconstruction.
- Utilizing drug metabolism prediction, quantitative structure-activity relationship (QSAR) models, and structural similarity searching.
- Mapping compounds and proteins to functional ontologies and reconstructing biological networks.
Main Results:
- Generation of lists of similar compounds and potential targets for novel compounds.
- Reconstruction of biologically-meaningful networks linking compounds, targets, and biological effects.
- Successful in silico evaluation of potential xenobiotic impacts on biological systems.
Conclusions:
- The integrated system provides early assessment of biological effects, aiding compound prioritization in drug discovery.
- It facilitates directed medicinal chemistry efforts to optimize compound activity and safety profiles.
- This approach enhances the efficiency of the drug discovery and development pipeline.
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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,...
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,...
02:26Protein 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,...
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,...
02:04Protein-protein Interfaces
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
02:04Protein-Protein Interfaces
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
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