Pharmacophore Modeling and Molecular Docking: Bridging the Gap Between Structure and Function
From Structure to Function: Accelerating Drug Discovery with Pharmacophore Modeling and Docking.
About This Course
Pharmacophore modeling identifies the essential features required for a molecule to bind to a specific biological target, while molecular docking simulates the interaction between small molecules (ligands) and target macromolecules (usually proteins) to predict binding affinity. These methods are key in the early stages of drug design, allowing researchers to virtually screen large libraries of compounds, optimize molecular interactions, and identify potential drug candidates.
This workshop will provide a comprehensive understanding of both pharmacophore modeling and molecular docking, teaching participants how to create pharmacophore models, perform docking studies, and analyze docking results. Participants will also learn to use popular tools for pharmacophore-based virtual screening and molecular docking simulations. Dry-lab sessions will cover software tools such as AutoDock, GOLD, and MOE and demonstrate practical workflows in computational drug discovery.
Aim
This workshop aims to teach participants the principles and applications of pharmacophore modeling and molecular docking for drug discovery. It covers how pharmacophore-based approaches can identify key functional groups and how docking techniques predict interactions between small molecules and macromolecular targets. The program emphasizes integrating structure-based approaches into drug design workflows, supporting researchers and professionals in drug discovery, computational chemistry, and molecular modeling.
Workshop Objectives
- Understand pharmacophore modeling concepts and its role in drug design.
- Learn molecular docking principles for ligand-target interaction predictions.
- Analyze and interpret docking results for binding affinity and molecular interactions.
- Use computational tools for virtual screening and hit identification.
- Apply pharmacophore modeling and docking simulations to design drug-like compounds.
Workshop Structure
Day 1: Introduction to Pharmacophore Modeling
- Pharmacophore Concept: What it is, and its role in drug discovery
- Pharmacophore Generation: Methods to create pharmacophore models (3D-QSAR, receptor-based, ligand-based)
- Tools: MOE, LigandScout, Discovery Studio
- Mini task: Generate a pharmacophore model for a selected drug target using LigandScout
Day 2: Molecular Docking Fundamentals
- Docking Theory: Docking algorithms, scoring functions, and their application in virtual screening
- Preparing Receptors and Ligands: Receptor preparation, ligand conformer generation, and energy minimization
- Key Analyses: Binding affinity, RMSD, and interaction profiles
- Tools: AutoDock Vina, PyRx, DockingServer
- Mini task: Perform molecular docking of a ligand with a receptor and analyze interaction scores and binding modes
Day 3: Advanced Applications and Research-Grade Reporting
- Advanced Docking: Induced fit docking, protein flexibility, and multi-target docking
- Binding Site Analysis: Identifying and visualizing active sites, interaction networks, and water-mediated interactions
- Pharmacophore-Docking Integration: Integrating pharmacophore models into docking workflows for virtual screening
- Reproducibility and Reporting: Best practices for reporting docking results and ensuring reproducibility in publications
- Tools: AutoDock, PyMOL, Chimera, and optional PLUMED overview
- Mini task: Create a 1-page research-grade docking report (including binding site visualization, ligand poses, and interaction analysis)
Who Should Enrol?
- Doctoral Scholars & Researchers: PhD candidates seeking to integrate computational workflows into their molecular research.
- Postdoctoral Fellows: Early-career scientists aiming to enhance their data-driven publication profile.
- University Faculty: Professors and HODs interested in modern bioinformatics pedagogy and tool mastery.
- Industry Scientists: R&D professionals from the Biotechnology and Pharmaceutical sectors transitioning to genomic-driven discovery.
- Postgraduate Students: Final-year PG students looking for specialized research-grade exposure beyond standard curricula.
Important Dates
Registration Ends
January 15, 2026
IST 07:00 PM
Workshop Dates
January 15, 2026 – January 17, 2026
IST 08:00 PM
Workshop Outcomes
Participants will be able to:
- Create and apply pharmacophore models to identify key binding features in drug design.
- Perform molecular docking studies to predict protein-ligand interactions.
- Interpret docking results and evaluate binding affinity for drug candidates.
- Conduct virtual screening using docking simulations for lead discovery.
- Understand the practical use of computational chemistry tools like AutoDock and MOE.
Recording fee
Participants in India
₹2,499
Participants outside India
$50
- All session recordings
- Study material
- Certificate after completion
- 1-year access
The live sessions of this workshop are over, so the live fees no longer apply. The recordings are being uploaded. They appear in your dashboard as soon as they are ready, and we will e-mail you then.
Frequently asked questions
Will I get the recording?
Yes. Paid participants get the session recordings and study material in their NanoSchool dashboard (My registrations → Recorded Lectures / Study Material).
What if I miss a live session?
Watch the recording in your dashboard and send your questions to the mentor through the support desk.
Do I get a certificate?
Yes, an e-certificate of participation after the workshop, with a QR code anyone can verify and an "Add to LinkedIn" button.
Which fee category applies to me?
Choose the category that matches your current role: Student, Ph.D. Scholar / Researcher, Academician / Faculty or Industry Professional.
How can I pay?
By card, UPI or PayPal on the payment page; international bank transfer is also available there.
What is the refund policy?
See our Returns, Refunds & Cancellation policy: Returns, Refunds & Cancellation policy
Registration open
More upcoming workshops
Live, mentor-led and certified. Dates and times in IST.
AI-Driven CNS Drug Discovery: AlphaFold 3, Molecular Docking, BBB-ADMET Screening & GROMACS Molecular Dynamics
- Dates
- 9–11 Nov 2026
- Time
- 5:00 PM IST
- Duration
- 3 Days
- Level
- Moderate
- Student₹2,499
- Ph.D. Scholar / Researcher₹3,499
- Academician / Faculty₹4,499
- Industry Professional₹5,499
AI-Guided RNA Epitranscriptomics: m6A Modification Profiling, RNA Regulatory Networks & Disease Biomarkers
- Dates
- 9–11 Nov 2026
- Time
- 5:30 PM IST
- Duration
- 3 Days
- Level
- Moderate
- Student₹3,000
- Ph.D. Scholar / Researcher₹4,000
- Academician / Faculty₹5,000
- Industry Professional₹7,000
Mitochondrial Genomics & Disease: mtDNA Variant Analysis and Precision Medicine
- Dates
- 10–12 Nov 2026
- Time
- 5:30 PM IST
- Duration
- 3 Days
- Level
- Moderate
- Student₹2,499
- Ph.D. Scholar / Researcher₹3,499
- Academician / Faculty₹4,999
- Industry Professional₹5,999
AI-Powered Metabolomics & Precision Medicine: Disease Biomarker Discovery, Multi-Omics Analysis & Machine Learning
- Dates
- 12–14 Nov 2026
- Time
- 5:30 PM IST
- Duration
- 3 Days
- Level
- Moderate
- Student₹2,299
- Ph.D. Scholar / Researcher₹3,399
- Academician / Faculty₹4,499
- Industry Professional₹5,999
Non-Coding RNA Therapeutics: miRNA, lncRNA & Disease Network Analysis
- Dates
- 12–14 Nov 2026
- Time
- 5:30 PM IST
- Duration
- 3 Days
- Level
- Moderate
- Student₹2,499
- Ph.D. Scholar / Researcher₹3,499
- Academician / Faculty₹4,999
- Industry Professional₹6,299
AI-Driven Drug Discovery: AlphaFold 3, Molecular Docking, ADMET & GROMACS
- Dates
- 12–14 Nov 2026
- Time
- 5:00 PM IST
- Duration
- 3 Days
- Level
- Moderate
- Student₹2,499
- Ph.D. Scholar / Researcher₹3,499
- Academician / Faculty₹4,499
- Industry Professional₹6,499






