Module #1 Introduction to Molecular Dynamics Simulations Overview of molecular dynamics simulations, importance in protein research, and brief history
Module #2 Basics of Protein Structure and Function Review of protein structure, folding, and function, including primary, secondary, tertiary, and quaternary structures
Module #3 Force Fields and Potential Energy Functions Introduction to force fields, potential energy functions, and their role in molecular dynamics simulations
Module #4 MD Simulation Algorithms and Integrators Overview of MD simulation algorithms, integrators, and their implementation
Module #5 Simulation Ensembles and Boundary Conditions Discussion of simulation ensembles, boundary conditions, and their effect on simulation outcomes
Module #6 Preparing a Protein for MD Simulation Protein preparation, including processing PDB files, adding hydrogen atoms, and protonating residues
Module #7 Setting Up an MD Simulation Configuring an MD simulation, including setting up the simulation box, selecting the force field, and defining the simulation protocol
Module #8 Running and Monitoring an MD Simulation Executing an MD simulation, monitoring its progress, and troubleshooting common issues
Module #9 Data Analysis and Visualization Introduction to analyzing and visualizing MD simulation data, including trajectory analysis and visualization tools
Module #10 Measuring Structural Properties Calculating and analyzing structural properties, such as RMSD, RMSF, and secondary structure
Module #11 Measuring Dynamic Properties Calculating and analyzing dynamic properties, such as diffusion coefficients, rotational correlatioms, and hydrogen bonding
Module #12 Free Energy Calculations Introduction to free energy calculations, including thermodynamic integration and free energy perturbation
Module #13 Protein-Ligand Interactions and Binding Free Energy Simulating protein-ligand interactions, calculating binding free energy, and predicting binding affinity
Module #14 Protein-Protein Interactions and Oligomerization Simulating protein-protein interactions, oligomerization, and analyzing protein-protein interfaces
Module #15 Enhanced Sampling Techniques Introduction to enhanced sampling techniques, including replica exchange, metadynamics, and accelerated molecular dynamics
Module #16 Simulating Protein Folding and Misfolding Simulating protein folding, misfolding, and aggregation, including simulation protocols and analysis tools
Module #17 Simulating Protein-Membrane Interactions Simulating protein-membrane interactions, including protein-lipid interactions and membrane protein diffusion
Module #18 High-Performance Computing for MD Simulations Introduction to high-performance computing, parallelization, and distributed computing for MD simulations
Module #19 Best Practices for MD Simulation and Analysis Best practices for MD simulation setup, execution, and analysis, including simulation validation and error estimation
Module #20 Case Studies in Protein MD Simulations Real-world examples of protein MD simulations, including applications in drug design, protein engineering, and biotechnology
Module #21 Advanced Topics in Protein MD Simulations Advanced topics, including QM/MM, path sampling, and machine learning applications in protein MD simulations
Module #22 MD Simulation Software and Tools Overview of popular MD simulation software and tools, including GROMACS, AMBER, NAMD, and VMD
Module #23 MD Simulation Analysis and Visualization Tools Introduction to MD simulation analysis and visualization tools, including PyMOL, Chimera, and MDAnalysis
Module #24 MD Simulation in Drug Discovery and Development Applications of MD simulations in drug discovery and development, including lead optimization and pharmacodynamics
Module #25 MD Simulation in Protein Engineering and Design Applications of MD simulations in protein engineering and design, including enzyme design and protein stability
Module #26 MD Simulation in Biotechnology and Biosensors Applications of MD simulations in biotechnology and biosensors, including protein-based biosensors and biofuel cells
Module #27 MD Simulation in Computational Biology and Bioinformatics Applications of MD simulations in computational biology and bioinformatics, including protein structure prediction and functional annotation
Module #28 MD Simulation in Materials Science and Nanotechnology Applications of MD simulations in materials science and nanotechnology, including protein-based materials and nanostructures
Module #29 MD Simulation in Biomedical Research and Medicine Applications of MD simulations in biomedical research and medicine, including understanding disease mechanisms and drug design
Module #30 Course Wrap-Up & Conclusion Planning next steps in Molecular Dynamics Simulations of Proteins career
