MD Simulation
Classical Molecular Dynamics (MD) is the main workflow for simulating biomolecular systems. MD simulates how atoms and molecules move over time by numerically solving Newton's equations of motion where the forces between atoms are approximated by an empirical force field. Physical accuracy (which would require quantum mechanics) is traded for computational cost letting us simulate proteins, solvent, and ligands.
Branches
git branch --listbace1-target-study
Inhibition of β-amyloid cleaving enzyme 1 (BACE1) is a promising approach to the treatment of Alzheimer's disease. Understanding the mechanisms of binding between inhibitors and BACE1 would help in designing more effective BACE1 inhibitors. We use GROMACS to run molecular dynamics simulations and gain an in-depth, atomic-level understanding of this binding process.
status: active