New Year Offer End Date: 29th February 2024

In Silico Molecular Modeling and Docking in Drug Development

Transforming Molecules into Medicine: Charting the Future of Drug Development through Molecular Modeling and Docking Strategies

About Workshop:

The clinical application of drugs in the treatment of diseases has been limited by severe toxic side effects during administration of the drugs. Thus, it has been the objective of numerous studies to prepare better and safe drugs. Molecular modelling and docking could be utilized for generation of effective drug agents (inhibitor) against disease (target) in computer Aided Drug Design (CADD). As a result of this, a large number of candidate drugs have been developed till now. These methods provide the data set for development of computational models, for virtual screening and prediction of biological activity of the new drug to be developed in the near future. These computational models also reduce the number of candidate molecules that needs to synthesized and tested, reducing both cost and time in the process of drug development.
Also, the above said techniques will provide a unique platform to all the researchers working in this field to screen new molecules which are synthesized. The main problem of any drug and other agents, which substantially reduces their therapeutic usefulness, lies in their scant selectivity because these substances affect diseased and normal cells alike and lead to the appearance of adverse side effects. This could be elucidated by exploring the mechanism and mode of action of these agents with the receptor to calculate the probabilities of their existence, leading to deciphering their interaction, mechanism and activity which are very essential for the development of better and safe drugs.

Aim: The aim of the workshop is to emphasize molecular modelling and drug/receptor interaction to explore biological phenomena at the molecular level. Traditional drug treatments often suffer from severe side effects, driving the pursuit of safer alternatives. Molecular modeling and docking, key to Computer-Aided Drug Design, enable the creation of effective drug agents, leading to a plethora of candidate drugs. These methods streamline drug development by providing essential datasets for computational models, virtual screening, and predicting biological activity, reducing costs and time in the process.

Course Objectives:

  • To understand the three-dimensional structures and their physicochemical properties of drugs and receptors.
  • To generate 3D structure from known raw sequence.
  • To design the drug based on known and unknown target.

What you will learn?

Day 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

Day 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

Day 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

Day 4: Structure Validation

  • Protein Structure validation
  • Ramachandran plot

Tools: SAVES server

Day 5: Docking and Interaction studies

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

Tools: PyRx & ArgusLab

Fee Plan

StudentINR 1399/- OR USD 50
Ph.D. Scholar / ResearcherINR 1699/- OR USD 55
Academician / FacultyINR 2199/- OR USD 60
Industry ProfessionalINR 2699/- OR USD 85

Intended For : Students, Faculty, and Researchers from Pharmaceutical Sciences, Bioinformatics, Computational Biology, Medicinal Chemistry, Structural Biology, Biotechnology, and Drug Discovery Research

Career Supporting Skills

Computational Drug Design Expertise Bioinformatics Proficiency Software and Tools Mastery Homology Modeling Proficiency Software Utilization like PyRx, ArgusLab, ISIS Draw, and ChemSketch

Course Outcomes

  • Mastery of Molecular Modeling: Attain a comprehensive understanding of three-dimensional structures and physicochemical properties of drugs and receptors.
  • Practical 3D Structure Generation: Acquire skills in generating 3D structures from raw sequence data using tools like ISIS Draw and ChemSketch.
  • In-depth Protein Insight: Gain an overview of protein structures, interaction with ligands, and active site prediction using Protein Data Bank (PDB) and relevant tools.
  • Advanced Modeling Techniques: Develop proficiency in comparative modeling and homology modeling, utilizing tools such as Modeller and online resources.
  • Structure Validation Expertise: Learn to validate protein structures using tools like the SAVES server and interpret results, including Ramachandran plot analysis.
  • Hands-On Docking Studies: Explore Structure-Based Drug Design (SBDD) and Ligand-Based Drug Design (LBDD) through practical exercises using PyRx and ArgusLab.
  • Strategic Drug Design: Understand the process of designing drugs based on known and unknown targets, bridging the gap between theory and application.
  • Enhanced Research Skills: Develop the ability to critically analyze molecular interactions, contributing to advancements in drug development and virtual screening.
  • Efficient Compound Library Preparation: Learn to prepare compound libraries, generate 2D and 3D structures, and calculate energy and molecular properties using various software tools.
  • Practical Application: Apply acquired knowledge in a real-world context, empowering participants to contribute to the field of drug development through computational approaches.