Module 1: Computer Aided Drug Design Modules
15 Days:
- Literature Search using various Bioinformatics resources.
- Retrieval of Primary Protein and Ligand details.
- Extensive Mutational Analysis.
- Molecular Modeling using the classical method and alpha fold.
- Molecular Docking Studies and statistical analysis.
1 Month (Following the 15 Days):
- All modules from the previous 15 days.
- Fundamentals of Molecular Dynamics Simulations using Protein & Protein-Ligand systems.
- Dissertation writing and Assesments of the internship.
Module 2: Molecular Dynamics Simulations Modules and topics
15 Days:
- Literature search using various Bioinformatics resources.
- Basics & fundamentals of Molecular Dynamics Simulations.
- Preparation, Equilibration, and Production run using a protein system.
- Post Molecular Dynamics (MD) analysis (Basic to Advanced).
- Report writing.
1 Month (Following the 15 Days):
- All modules from the previous 15 days.
- Retrieval of Primary Protein and Ligand details.
- Molecular Docking Studies and statistical analysis.
- Preparation, Equilibration, Production run using Protein & Protein-Ligand systems.
- Post MD analysis (Basic to Advanced).
- Dissertation writing and evaluation of the internship.
Module 3: CHARMM-GUI: Membrane Dynamics Simulations Modules and topics
15 Days:
- Introduction to types of membrane proteins and Lipid force fields.
- Introduction to CHARMM-GUI and OPM servers.
- PDB reader and manipulator for reading PDB and PDBx/mmCIF structure files and modifying side chains.
- The parameterization of ligands & HETATM.
- Orientation of the protein along the membrane and system building using CHARMM-GUI.
- Membrane Builder for generating a bilayer, followed by the preparation of files for Molecular Dynamics (MD) simulations.
1 Month (Following the 15 Days):
- All modules from the previous 15 days.
- Basics and fundamentals of Molecular Dynamics Simulations.
- Preparation, Equilibration, Production run using a Protein system.
- Post-MD analysis (Basic to Advanced).
- Dissertation writing and various internship assessments.