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.
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