Biomolecular Modeling and Simulation
( 25 Modules )

Module #1
Introduction to Biomolecular Modeling
Overview of biomolecular modeling, importance, and applications

Module #2
Biomolecular Structure and Function
Review of biomolecular structures, including proteins, nucleic acids, lipids, and carbohydrates

Module #3
Molecular Mechanics and Force Fields
Introduction to molecular mechanics, force fields, and potential energy functions

Module #4
Molecular Dynamics Simulation
Principles and algorithms of molecular dynamics simulation, including integration methods and ensemble averages

Module #5
Monte Carlo Simulation
Principles and algorithms of Monte Carlo simulation, including random number generation and sampling methods

Module #6
Biomolecular Force Fields
Introduction to popular biomolecular force fields, including AMBER, CHARMM, and OPLS

Module #7
Simulation Software
Overview of popular simulation software, including GROMACS, AMBER, and NAMD

Module #8
Protein Structure Prediction
Introduction to protein structure prediction methods, including ab initio and template-based approaches

Module #9
Protein-Ligand Interactions
Simulation of protein-ligand interactions, including docking and molecular dynamics

Module #10
Free Energy Calculations
Introduction to free energy calculations, including thermodynamic integration and free energy perturbation

Module #11
Enhanced Sampling Methods
Introduction to enhanced sampling methods, including replica exchange and umbrella sampling

Module #12
Coarse-Grained Modeling
Introduction to coarse-grained modeling, including lattice models and bead models

Module #13
QMMM Modeling
Introduction to quantum mechanics/molecular mechanics (QMMM) modeling

Module #14
Simulation of Biomolecular Systems
Simulation of biomolecular systems, including membranes, lipids, and nucleic acids

Module #15
Simulation of Biological Processes
Simulation of biological processes, including protein folding, binding, and enzymatic reactions

Module #16
Analysis of Simulation Data
Introduction to analysis of simulation data, including visualization, clustering, and statistical methods

Module #17
Validation of Simulation Results
Validation of simulation results, including comparison to experimental data and benchmarking

Module #18
High-Performance Computing for Biomolecular Simulation
Introduction to high-performance computing for biomolecular simulation, including parallelization and optimization

Module #19
Biomolecular Modeling for Drug Discovery
Applications of biomolecular modeling in drug discovery, including virtual screening and lead optimization

Module #20
Biomolecular Modeling for Biotechnology
Applications of biomolecular modeling in biotechnology, including protein engineering and biocatalysis

Module #21
Biomolecular Modeling for Systems Biology
Applications of biomolecular modeling in systems biology, including network modeling and systems simulation

Module #22
Case Studies in Biomolecular Modeling
In-depth case studies of biomolecular modeling applications in various fields

Module #23
Best Practices in Biomolecular Modeling
Best practices in biomolecular modeling, including model validation, simulation protocols, and data analysis

Module #24
Future Directions in Biomolecular Modeling
Future directions in biomolecular modeling, including machine learning, artificial intelligence, and multi-scale modeling

Module #25
Course Wrap-Up & Conclusion
Planning next steps in Biomolecular Modeling and Simulation career

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Biomolecular Modeling and Simulation ( 25 Modules )

Biomolecular Modeling and Simulation
( 25 Modules )