Molecular Dynamics Simulations of Proteins
( 30 Modules )

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

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Molecular Dynamics Simulations of Proteins ( 30 Modules )

Molecular Dynamics Simulations of Proteins
( 30 Modules )