7-Days Online Faculty Development Program on Computer Aided Drug Design (Hands-on-Training) |CADD|

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• Daily 1.0 Hr session for 7 Days.
• Recordings will be shared after every Live session.

Detailed Day wise Schedule

2 Jan. 2023: Day 1 - Session 1: By Dr.   Nikhil Aggarwal, HOD [ACC]

• Introduction to Bioinformatics, Role of Pharmacology in Drug Discovery  CADD, Overview of the process of   drug discovery
• CADD Software Tools Installation
• Understanding file formats (sdf, mol,   pdb)

3 Jan. 2023: Day 2 - Session  2: By Dr. Nikhil   Aggarwal, HOD [ACC]

Structure   based Drug Design (target-ligand docking)

• Online Database Exploration (PubMed,   PubChem, RCSB-PDB, etc.)
• Introduction   to Structure based Drug Design and process layout of Docking
• Comparative   modelling of protein (Homology modelling)
• Thermodynamical   criteria
• Molecular   Docking using Autodock vina/Autodock Tools/PyRx (For docking of multiple   ligands)
• Protein   file preparation: removal of side moieties, repairing of polypeptide chains, Docking   studies: Protein structure input file preparation: removal of water, polar   hydrogens, charge neutralization

4 Jan. 2023: Day 3 - Session 3: By Dr.   Nikhil Aggarwal, HOD [ACC]

• Ligand file preparation: polar   hydrogens, charge neutralization, labelling of aromatic carbons and rotationable   bonds
• Setting grid parameters and Docking   parameters: Blind docking vs site-specific docking, saving grid dimensions
• Setting and executing the calculation.

5 Jan. 2023: Day 4 - Session 4: By Dr.   Nikhil Aggarwal, HOD [ACC]

• Docking   analysis: Understanding how   drugs function at the molecular level.
• Based   on binding energy, Hydrogen bond interactions, electrostatic interactions,   hydrophobic interactions, etc.)
• BINANA   (binding analyser)
• Pdbsum   for visualising protein-ligand interactions
• Building   protein-ligand complex and visualization (publication standard)

6 Jan. 2023: Day 5 - Session 5: By Dr.   Nikhil Aggarwal, HOD [ACC]

Molecular   Dynamics(MD) Simulation

• Introduction to Molecular Dynamics Simulations and related input parameters
• Basic   Principles of Molecular Dynamics Simulations (Non-bonded interactions, Bonding   Potentials, Force fields)
• Molecular Dynamics Simulation using GROMACS/VMD-NAMD
• Installation of softwares required for simulations

7 Jan. 2023: Day 6 -  Session 6: By Dr.   Nikhil Aggarwal, HOD [ACC]

• Definition of molecular structures
• Understanding configuration files
• Protein structure Determination (Topology File) 2D and 3D Surface mapping using Molecular Simulation via GROMACS   software
• Protein-water interaction
• Preparation of files: Force field   and topology
• Simulation (Energy Minimization, Heating,   NVT & NPT Equilibration, Production)

8 Jan. 2023: Day 7 - Session 7: By Dr.   Nikhil Aggarwal, HOD [ACC]

• Analysis of results: Protein-Ligand Docking,   visualization of molecular dynamics via VMD.

Salient Features:

• Eligibility: Candidate must have knowledge of science  (not less than under-graduation level)
• FDP will be taken via online mode: Platform-Zoom
• Registered candidates can submit a short report (template will be provide) for further screening
• E-certificates will be provided to all registered participants
• Training will be provided on Windows Operating system
• Programming and coding knowledge is not required for above FDP.
• Lecture Mode: English