Molecular Dynamic Simulations for Drug Discovery

Explore molecular dynamics simulations as a computer method to model atomic movements, reveal conformational changes and protein–ligand interactions relevant to drug discovery, and analyze structure dynamics and thermodynamics.

Explore the opls force field, a set of equations that assign mass, geometry, and interaction properties to each atom, enabling bonded and nonbonded interactions in protein conformational changes during simulations.

Learn the molecular dynamics timescale from femtoseconds to seconds and decide simulation length based on the research question. Identify durations to capture vibrational motions, rotational motions, and protein folding.

Learn to download and install Schrodinger's Desmond module for molecular dynamics simulations, configure licensing, GPUs, and launch Maestro for running and analyzing results.

Learn how to prepare a protein for molecular dynamics, including importing the PDB, adding hydrogens, removing unwanted water, repairing missing residues, minimizing clashes, and optimizing the structure for MD simulations.

Set up and run a molecular dynamics simulation by preparing the protein, solvating it with a chosen solvent, adding ions, minimizing energy, and configuring temperature, pressure, and trajectory output.

Analyze trajectory outputs from molecular dynamics simulations to assess simulation quality, energy stability, and protein-ligand interactions, while monitoring temperature, pressure, and volume for reliable results.

Analyze protein-ligand interactions from molecular dynamics outputs, loading trajectory files and generating interaction diagrams to identify hydrogen bonds, hydrophobic, van der waals, and electrostatic contacts; assess stability and conformational changes.