Self Paced

In Silico Molecular Modeling and Docking in Drug Development

Transforming Drug Discovery with Computational Precision

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Online/ e-LMS
Self Paced
1 Month


In silico molecular modeling and docking play a crucial role in modern drug development by enabling the prediction and analysis of molecular interactions between drug candidates and their biological targets. This program covers both the theoretical foundations and practical applications of these techniques, focusing on molecular dynamics, binding site identification, and virtual screening. Participants will learn to use various software tools and databases, perform molecular modeling and docking studies, and interpret the results to inform drug design.

Throughout the one-month program, participants will engage in hands-on sessions and projects that simulate real-world drug discovery scenarios. They will gain experience in setting up and running molecular simulations, analyzing docking results, and optimizing drug candidates based on computational predictions. By the end of the program, participants will be proficient in using in silico methods to enhance the efficiency and effectiveness of drug development processes, making them valuable assets in pharmaceutical and biotechnology industries.


The program aims to equip participants with comprehensive knowledge and practical skills in in silico molecular modeling and docking techniques. This knowledge will be essential for accelerating the drug discovery process and optimizing drug candidates through computational methods.

Program Objectives

  • Understand the principles of molecular modeling and docking.
  • Master the use of computational tools for drug discovery.
  • Perform virtual screening and binding site analysis.
  • Interpret docking results and optimize drug candidates.
  • Apply in silico techniques to real-world drug development projects.

Program Structure

Module 1: Preparation of Protein Structure

Preparation of compound library

  • Generating the 2D structure
  • Generating the 3D structure

Energy and molecular properties calculation

  • Force field and Energy minimization
  • Properties based on Quantum Mechanics


  • ISIS Draw/ChemSketch
  • Argus Lab
  • Mopac

Module 2: Protein active site prediction

Overview of Protein and their interaction with ligand

  • Overview of protein 3D structure file format
  • Overview of small molecule databases

Protein Active site

  • Protein Active site Properties
  • Protein active site prediction


  • Protein Data Bank (PDB)/PDBSum
  • PubChem/Drug Bank/Zinc Database
  • Active site prediction tool

Module 3: Comparative modeling/homology modeling

  • Protein 3D structure Prediction based on homology
  • Ab initio structure prediction

Tools: Modeller & Online Tools for Ab initio structure prediction

Module 4: Structure Validation

  • Protein Structure validation
  • Ramachandran plot

Tools: SAVES server

Module 5: Docking and Interaction studies

  • Structure Based Drug Design (SBDD)
  • Ligand Based Drug Design (LBDD)

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 with a keen interest in drug discovery 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 the drug discovery process with advanced in silico techniques.

Fee Structure

Standard Fee:           INR 4,998           USD 110

Discounted Fee:       INR 2499             USD 55





Program Assessment

Certification to this program will be based on the evaluation of following assignment (s)/ examinations:

Exam Weightage
Mid Term Assignments 20 %
Final Online Exam 30 %
Project Report Submission (Includes Mandatory Paper Publication) 50 %

To study the printed/online course material, submit and clear, the mid term assignments, project work/research study (in completion of project work/research study, a final report must be submitted) and the online examination, you are allotted a 1-month period. You will be awarded a certificate, only after successful completion/ and clearance of all the aforesaid assignment(s) and examinations.

Program Deliverables

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

Future Career Prospects

  • Computational Chemist
  • Drug Design Scientist
  • Molecular Modeler
  • Pharmacologist
  • Research Scientist in Pharmaceutical Companies
  • Bioinformatics Specialist

Enter the Hall of Fame!

Take your research to the next level!

Publication Opportunity
Potentially earn a place in our coveted Hall of Fame.

Centre of Excellence
Join the esteemed Centre of Excellence.

Networking and Learning
Network with industry leaders, access ongoing learning opportunities.

Hall of Fame
Get your groundbreaking work considered for publication in a prestigious Open Access Journal (worth ₹20,000/USD 1,000).

Achieve excellence and solidify your reputation among the elite!


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