4 Modeling and Simulation

4.1 Molecular Modeling and Dynamics

4.1.1 Key Concepts

Protein Structure Prediction
Molecular Docking
Molecular Dynamics Simulations
Free Energy Calculations
Protein-Ligand Interactions

4.1.2 Recommended Resources

Tools and Software:
- GROMACS - Molecular Dynamics
- AutoDock - Molecular Docking
- PyMOL - Molecular Visualization
- AMBER - Molecular Dynamics
Learning Resources:
- GROMACS Tutorials
- Molecular Dynamics Course

4.2 Systems Biology

4.2.1 Key Concepts

Mathematical Modeling of Biological Systems
Network Analysis
Dynamic Systems
Metabolic Network Modeling
Cell Signaling Networks

4.2.2 Recommended Resources

Tools and Software:
- COPASI - Biochemical Network Simulator
- CellDesigner - Network Modeling
- SBML - Systems Biology Markup Language
- BioNetGen - Rule-based Modeling
Learning Resources:
- Systems Biology Course
- COPASI Tutorials

4.3 Computational Ecology, Evolution and Phylogenetics

4.3.1 Key Concepts

Phylogenetic Tree Construction
Population Genetics
Evolutionary Analysis
Ecological Modeling
Species Distribution Modeling

4.3.2 Recommended Resources

Tools and Software:
- BEAST2 - Bayesian Evolutionary Analysis
- RAxML - Phylogenetic Analysis
- BEAST - Bayesian Evolutionary Analysis
- PhyloBayes - Bayesian Phylogenetic Inference
Learning Resources:
- Phylogenetics Course
- BEAST2 Tutorials

4.4 Computational Pharmacology and Drug Design

4.4.1 Key Concepts

Structure-Based Drug Design
Virtual Screening
ADME/Tox Prediction
Pharmacophore Modeling
Drug-Target Interactions

4.4.2 Recommended Resources

Tools and Software:
- OpenEye - Drug Design Software
- Schrödinger - Drug Discovery Platform
- MOE - Molecular Operating Environment
- RDKit - Cheminformatics Toolkit
Learning Resources:
- Drug Design Course
- RDKit Tutorials

4.5 Mathematical Modeling of Biological Systems

4.5.1 Key Concepts

Differential Equations
Stochastic Modeling
Agent-Based Modeling
Spatial Modeling
Multi-Scale Modeling

4.5.2 Recommended Resources

Tools and Software:
- MATLAB - Numerical Computing
- Python SciPy - Scientific Computing
- R - Statistical Computing
- NetLogo - Agent-Based Modeling
Learning Resources:
- Mathematical Biology Course
- Python for Scientific Computing

# Modeling and Simulation ## Molecular Modeling and Dynamics ### Key Concepts - Protein Structure Prediction - Molecular Docking - Molecular Dynamics Simulations - Free Energy Calculations - Protein-Ligand Interactions ### Recommended Resources - **Tools and Software**: - [GROMACS](https://www.gromacs.org/) - Molecular Dynamics - [AutoDock](http://autodock.scripps.edu/) - Molecular Docking - [PyMOL](https://pymol.org/) - Molecular Visualization - [AMBER](https://ambermd.org/) - Molecular Dynamics - **Learning Resources**: - [GROMACS Tutorials](https://www.gromacs.org/Documentation/Tutorials) - [Molecular Dynamics Course](https://www.ebi.ac.uk/training/online/courses/molecular-dynamics/) ## Systems Biology ### Key Concepts - Mathematical Modeling of Biological Systems - Network Analysis - Dynamic Systems - Metabolic Network Modeling - Cell Signaling Networks ### Recommended Resources - **Tools and Software**: - [COPASI](https://copasi.org/) - Biochemical Network Simulator - [CellDesigner](https://www.celldesigner.org/) - Network Modeling - [SBML](http://sbml.org/) - Systems Biology Markup Language - [BioNetGen](https://bionetgen.org/) - Rule-based Modeling - **Learning Resources**: - [Systems Biology Course](https://www.ebi.ac.uk/training/online/courses/systems-biology/) - [COPASI Tutorials](https://copasi.org/Support/Tutorials/) ## Computational Ecology, Evolution and Phylogenetics ### Key Concepts - Phylogenetic Tree Construction - Population Genetics - Evolutionary Analysis - Ecological Modeling - Species Distribution Modeling ### Recommended Resources - **Tools and Software**: - [BEAST2](https://www.beast2.org/) - Bayesian Evolutionary Analysis - [RAxML](https://cme.h-its.org/exelixis/web/software/raxml/) - Phylogenetic Analysis - [BEAST](https://beast.community/) - Bayesian Evolutionary Analysis - [PhyloBayes](http://www.phylobayes.org/) - Bayesian Phylogenetic Inference - **Learning Resources**: - [Phylogenetics Course](https://www.ebi.ac.uk/training/online/courses/phylogenetics/) - [BEAST2 Tutorials](https://www.beast2.org/tutorials/) ## Computational Pharmacology and Drug Design ### Key Concepts - Structure-Based Drug Design - Virtual Screening - ADME/Tox Prediction - Pharmacophore Modeling - Drug-Target Interactions ### Recommended Resources - **Tools and Software**: - [OpenEye](https://www.eyesopen.com/) - Drug Design Software - [Schrödinger](https://www.schrodinger.com/) - Drug Discovery Platform - [MOE](https://www.chemcomp.com/) - Molecular Operating Environment - [RDKit](https://www.rdkit.org/) - Cheminformatics Toolkit - **Learning Resources**: - [Drug Design Course](https://www.ebi.ac.uk/training/online/courses/drug-design/) - [RDKit Tutorials](https://www.rdkit.org/docs/GettingStartedInPython.html) ## Mathematical Modeling of Biological Systems ### Key Concepts - Differential Equations - Stochastic Modeling - Agent-Based Modeling - Spatial Modeling - Multi-Scale Modeling ### Recommended Resources - **Tools and Software**: - [MATLAB](https://www.mathworks.com/products/matlab.html) - Numerical Computing - [Python SciPy](https://scipy.org/) - Scientific Computing - [R](https://www.r-project.org/) - Statistical Computing - [NetLogo](https://ccl.northwestern.edu/netlogo/) - Agent-Based Modeling - **Learning Resources**: - [Mathematical Biology Course](https://www.ebi.ac.uk/training/online/courses/mathematical-biology/) - [Python for Scientific Computing](https://scipy-lectures.org/)