Workshop on Compound-Target Interaction Network Design and Structure

The workshop on Compound-Target Interaction Network Design and Structure is tailored for students, researchers, and industry professionals in biotechnology, pharmaceuticals, and related fields. It highlights the application of bioinformatics tools in constructing and analyzing interaction networks, with a focus on understanding compound-target relationships, system biology insights, and therapeutic discovery. Participants will acquire theoretical knowledge and practical expertise in leveraging bioinformatics for compound-target interaction studies.

To equip participants with the skills and understanding required to design, construct, and analyze compound-target interaction networks, fostering innovation in drug discovery and therapeutic research.

Day 1: Fundamentals and Target Data Retrieval Introduction to Compound-Target Interaction Networks

• Overview and significance in drug discovery and system biology
• Briefing on workshop agenda and outcomes

Target Data Retrieval

• Exploring compound-target interaction databases (e.g., PubChem, DrugBank)
• Techniques for efficient data filtering and organization

Hands-On Session

• Practical walkthrough on retrieving and processing target data using online databases

Day 2: Network Construction and Analysis Building Compound-Target Networks

• Introduction to tools like Cytoscape and STRING
• Data integration and visualization techniques

Network Analysis Using CytoNCA

• Key metrics: degree centrality, betweenness centrality, and clustering coefficient
• Identifying critical nodes and hub targets

Hands-On Session

• Practical exercises on constructing and analyzing networks
• Interpretation of network properties and biological relevance

Day 3: Functional Enrichment and Network Visualization Pathway and Gene Ontology Analysis

• Introduction to Gene Ontology (GO) terms and pathway analysis concepts
• Importance of functional enrichment in drug discovery

Functional Enrichment with ClueGO

• Setting up and using the ClueGO plugin in Cytoscape
• Analysis and interpretation of enriched GO terms and pathways

Advanced Visualization Techniques

• Enhancing network aesthetics and information clarity
• Integrating functional enrichment results with networks

Hands-On Session

• Practical demonstrations on GO and pathway analysis
• Creating publication-ready network visualizations

Requirements

• Hardware: Windows PC or laptop with stable internet connectivity
• Software:
  • Cytoscape (latest version)
  • Plugins: ClueGO, CytoNCA
  • Additional tools as required (e.g., STRING database access)