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Protein Networks

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,...

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Updated: Jan 10, 2026

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling

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NeXus: An Automated Platform for Network Pharmacology and Multi-Method Enrichment Analysis.

Teh Bee Ping¹, Mohammad Alia², Bintang Annisa Bagustari³

¹Herbal Medicine Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam 40170, Malaysia.

International Journal of Molecular Sciences

|November 27, 2025

Summary

NeXus v1.2 automates network pharmacology and multi-method enrichment analysis, significantly reducing processing time and enhancing biological network analysis. This platform integrates complex drug-target interactions and pathways for efficient research.

Keywords:

GSEA GSVA ORA automated analysis bioinformatics data visualization drug discovery enrichment analysis multi-layer network network pharmacology pathway analysis systems biology traditional medicine

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Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation

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Published on: August 21, 2019

Area of Science:

Computational Biology
Bioinformatics
Systems Pharmacology

Background:

Network pharmacology is crucial for understanding complex biological systems but often hindered by manual processes and limited analytical integration.
Existing tools lack comprehensive capabilities for multi-layer biological relationship analysis and automated enrichment assessments.

Purpose of the Study:

To introduce NeXus v1.2, an automated platform designed to streamline network pharmacology and multi-method enrichment analysis.
To address limitations in existing tools by providing integrated analysis of gene, compound, and plant interactions.

Main Methods:

Implemented Over-Representation Analysis (ORA), Gene Set Enrichment Analysis (GSEA), and Gene Set Variation Analysis (GSVA) for robust enrichment analysis.
Validated NeXus v1.2 using datasets ranging from 111 to 10,847 genes, assessing scalability and performance.
Automated the generation of network maps, enrichment analyses, and relationship patterns with publication-quality visualizations.

Main Results:

NeXus v1.2 demonstrated robust scalability, handling large datasets efficiently with completion times under 3 minutes.
The platform reduced analysis time by over 95% compared to manual workflows, processing complex datasets in under 5 seconds.
Automated handling of incomplete data and maintenance of analytical integrity across biological layers were achieved.

Conclusions:

NeXus v1.2 offers a user-friendly and efficient platform for automated network pharmacology and complex biological network analysis.
The tool's modular architecture supports future integration of AI technologies and expansion into diverse therapeutic applications.
NeXus v1.2 significantly enhances automation and integration, providing a powerful solution for biological network research.