BS7107 - Computational Biology & Modelling

Availability: Semester 2

In this subject basic ideas for understanding biological phenomena using principles from underlying physical and chemical foundations used in computer modelling approaches are introduced. Emphasis will be on how these computational tools are applied to biological areas such as protein folding, membrane fusion, enzyme activity, drug-target interaction. These methods are illustrated with modern computer based laboratory practicals with graphical display of biological molecules. A variety of computational methods and modeling strategies are introduced, such as classical force field based on quantum theory and coarse grained models. Basic sampling techniques, such as Monte Carlo, molecular dynamics and Langevin dynamics simulation will be described.

Topics:

1. Energy, Forces and Dynamics
2. Potential Energy Functions, quantum mechanically and classically
3. Minimization method
4. Monte Carlo Simulation, sampling method 1
5. Molecular Dynamics Simulation , sampling method 2
6. Docking method, Predict Protein-drug structure
7. Scoring, Predict protein-drug binding energy
8. Modeling water, ions interaction