In Silico Molecular Modeling and Docking in Drug Development Course

About

In silico molecular modeling and docking are a key part of modern drug discovery because they help predict—and clearly explain—how a potential drug may bind with its biological target. This program blends the essential theory with practical, hands-on training, focusing on molecular dynamics, binding site identification, and virtual screening. You’ll use widely adopted software tools and trusted databases to run molecular modeling and docking studies, then learn how to interpret your results in a way that supports stronger, more confident drug design decisions.

Throughout this one-month program, you’ll work through guided hands-on sessions and mini-projects that mirror real-world drug development workflows. You’ll learn how to set up simulations, evaluate docking scores and interaction profiles, and optimize drug candidates using computational predictions. By the end, you’ll be able to apply in silico molecular modeling and docking to improve the speed and efficiency of drug development—valuable skills for careers in pharmaceutical and biotechnology teams.

Aim

The program aims to equip participants with practical skills and strong conceptual understanding in in silico molecular modeling and docking. This knowledge is essential for accelerating drug discovery, improving virtual screening outcomes, and optimizing drug candidates using reliable computational methods.

Program Objectives

• Understand the core principles of molecular modeling and molecular docking.
• Build confidence using computational tools that support in silico drug discovery.
• Perform virtual screening and binding site analysis using a structured workflow.
• Interpret docking results, analyze binding interactions, and optimize drug candidates.
• Apply in silico techniques to real-world drug development projects and case-style scenarios.

Program Structure

Module 1: Preparation of Protein Structure

• Prepare a compound library for screening
• Generate the 2D structure of drug-like molecules
• Generate the 3D structure for docking studies
• Calculate energy and key molecular properties
• Apply force fields and perform energy minimization
• Evaluate properties based on Quantum Mechanics

Tools: ISIS Draw/ChemSketch, Argus Lab, and Mopac

Module 2: Protein active site prediction

• Understand proteins and how they interact with ligands
• Learn common protein 3D structure file formats
• Explore popular small molecule databases used in drug discovery
• Perform protein active site prediction for docking preparation

Tools: Protein Data Bank (PDB)/PDBSum, PubChem/Drug Bank/Zinc Database, and Active site prediction tool

Module 3: Comparative modeling/homology modeling

• Predict protein 3D structure using homology (comparative) modeling
• Introduction to ab initio structure prediction approaches

Tools: Modeller & Online Tools for Ab initio structure prediction

Module 4: Structure Validation

• Validate protein structure quality using standard checks
• Interpret Ramachandran plots for structure assessment

Tools: SAVES server

Module 5: Docking and Interaction studies

• Structure Based Drug Design (SBDD): docking using target structure
• Ligand Based Drug Design (LBDD): learning from known active compounds

Tools: PyRx & ArgusLab

Participant’s Eligibility

• Undergraduate degree in Bioinformatics, Biotechnology, Chemistry, Pharmaceutical Sciences, or related fields.
• Professionals working in pharmaceutical or biotechnology industries.
• Individuals interested in drug discovery, molecular docking, and computational modeling.

Program Outcomes

• Participants will gain expertise in molecular modeling and docking, enabling them to design and optimize drug candidates using computational methods.
• They will be able to perform virtual screening, analyze binding interactions, and contribute to drug discovery using advanced in silico techniques.

Program Deliverables

• Access to e-LMS
• Real-Time Project for Dissertation
• Project Guidance
• Paper Publication Opportunity
• Self Assessment
• Final Examination
• e-Certification
• e-Marksheet