Map the Molecular Web – From Data to Discovery
10-Module Bioinformatics & Network Pharmacology Course
Three days. One end-to-end scientific pipeline. Endless research possibilities. Join live online from anywhere globally: from screening >1,100 candidate phytochemicals in HERB and SwissADME ADMET profiling to Cytoscape PPI hub screening, GO/KEGG pathway enrichment, AutoDock docking, and Molecular Dynamics (MD) trajectory analysis.
DR. KULDEEP SINGH
Ph.D. Biomedical Sciences (2026)
Dr. Kuldeep Singh’s doctoral research focused on deciphering the molecular mechanisms linking the gut microbiota-derived metabolite trimethylamine N-oxide (TMAO) with atherosclerosis and thrombus formation.
His research integrates biophysical experiments, biochemical assays, molecular docking, and molecular dynamics simulations with network pharmacology to validate multi-target therapeutic candidates.
10-Module Curriculum Breakdown
Explore the central scientific question, detailed topics, and key conceptual takeaways for each module.
Module 1: Introduction to Network Pharmacology & Bioinformatics Tools
"What are HERB, GeneCards, STRING and Cytoscape, and why do we use them?"
Understand the core principles of bioinformatics, network pharmacology, and how public repositories interconnect in one unified research workflow.
Module 2: Phytochemical / Drug Selection for Disease Targeting
"Which compounds are associated with the disease of interest?"
Screen and curate large compound libraries, retrieve candidate bioactive ingredients, and map them to known molecular targets.
Module 3: ADME & Drug-Likeness Screening Using SwissADME
"Which compounds have suitable predicted pharmacokinetic properties?"
Filter candidate phytochemicals based on physicochemical properties, GI absorption, blood-brain barrier permeability, and drug-likeness rules.
Module 4: Common Gene Identification Using Cytoscape
"Which genes are shared between compounds and disease?"
Intersect compound-target genes with disease-related genes using set intersection, Venn representations, and Cytoscape bipartite networks.
Module 5: Identification of Disease-Associated Genes Using GeneCards
"Which disease-associated genes have stronger database-level evidence?"
Query, rank, and prioritize human disease-associated genes using GeneCards relevance and evidence scores.
Module 6: Protein–Protein Interaction Network Analysis Using STRING
"How are the disease-associated proteins connected?"
Build topological Protein–Protein Interaction networks in STRING, evaluate interaction confidence, and calculate network statistics.
Module 7: Selection of Phytochemical–Target Hub Genes
"Which phytochemical-associated genes overlap with network hubs?"
Bridge phytochemical targets with topological PPI hubs to uncover critical shared nodes regulating disease pathways.
Module 8: Pathway & Functional Analysis
"What biological processes and pathways are represented?"
Perform Gene Ontology (GO) and KEGG / Reactome pathway enrichment to connect network hubs to verifiable biological mechanisms.
Module 9: Molecular Docking of Phytochemicals With Hub-Protein Targets
"Can a compound plausibly interact with a selected protein structure?"
Perform in silico molecular docking to evaluate candidate binding poses, binding free energy, and residue-level intermolecular interactions.
Module 10: Molecular Dynamics & Computational Validation
"Is the protein–ligand system dynamically stable and what interactions persist?"
Subject protein–ligand complexes to molecular dynamics simulations to evaluate thermodynamic stability, conformational drift, and flexibility.
3-Day Daily Schedule & Milestones
Day 1: Foundations, Library Screening & ADME Prioritization
Master bioinformatics database integration, screen >1,100 raw phytochemical libraries from HERB, and apply SwissADME pharmacokinetic filters to prioritize 30 lead candidates.
Day 2: Target Intersection, GeneCards & PPI Hub Gene Screening
Mine disease genetics with GeneCards, construct Cytoscape target intersection networks, evaluate STRING PPI interactomes, and isolate 10 core shared hub genes (TNF, IL6, NFKB1, etc.).
Day 3: Pathway Enrichment, Molecular Docking & MD Simulation
Perform GO/KEGG functional enrichment, test the ROS–NF-κB inflammatory axis, execute AutoDock molecular docking, and validate structural stability using Molecular Dynamics (RMSD/RMSF/Rg).
Databases & Software Covered
Workshop Ended
The live cohort for 25 – 27 September 2026 has concluded. Registrations are now closed.
Workshop Ended
Live Sessions Ended (25 – 27 Sept 2026)·Next Cohort Opening Soon
Thank you for the tremendous response!
The live sessions for Map the Molecular Web: Network Pharmacology Bootcamp have successfully concluded. Registrations are currently closed.
If you were an enrolled participant and need access to resources, recordings, or verified certificates, please contact our support team.