Pharmacophore Modeling and Molecular Docking: Bridging the Gap Between Structure and Function
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Course Overview
Program Syllabus
Module 1
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.
Module 2
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.
Module 3
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.
Module 4
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
Module 5
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
Module 6
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)
Module 7
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.
Module 8
Important Dates
Module 9
Registration Ends
01/15/2026
IST 07:00 PM
Module 10
Workshop Dates
01/15/2026 ā 01/17/2026
IST 08:00 PM
Module 11
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.
Module 12
Fee Structure
Module 13
Student Fee
ā¹1799 | $70
Module 14
Ph.D. Scholar / Researcher Fee
ā¹2799 | $80
Module 15
Academician / Faculty Fee
ā¹3799 | $95
Module 16
Industry Professional Fee
ā¹4799 | $110
Module 17
What You’ll Gain
- Live & recorded sessions
- e-Certificate upon completion
- Post-workshop query support
- Hands-on learning experience
Module 18
Join Our Hall of Fame!
Take your research to the next level with NanoSchool.
Module 19
Publication Opportunity
Get published in a prestigious open-access journal.
Module 20
Centre of Excellence
Become part of an elite research community.
Module 21
Networking & Learning
Connect with global researchers and mentors.
Module 22
Global Recognition
Worth ā¹20,000 / $1,000 in academic value.
Module 23
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