Molecular Modelling and Structure-based Drug Design, offered by the
University of Leeds, is one of a number of online courses run jointly
with The University of Manchester.
Our distance courses are delivered in a Virtual Learning Environment,
which allows us to extend the classroom into the web. Each course,
which is paced to suit those in full-time employment, runs over 16
teaching weeks.
This course is divided into 7 sections as follows:-
1. Molecular Mechanics
a. The molecular potential energy function
b. The empirical force field
c. Sources of force field data
d. Some examples of important force fields
2. Energy Minimisation
a. First derivative techniques: steepest descent and conjugate gradients
b. Second derivative techniques: Hessian matrix and Newton-Raphson
c. Global optimisation (simulated annealing, Tabu search, genetic
algorithms)
3. Molecular Dynamics and Monte Carlo Simulations
a. Brief introduction to statistical mechanics
b. Molecular dynamics simulations
c. Monte Carlo simulations
4. Conformational Analysis
a. Systematic methods
b. Random search methods
c. Distance geometry
d. Molecular dynamics
5. Solvation
a. Brief comparison of different solvation methods
b. Periodic boundary conditions
6. Calculation of Thermodynamics Parameters
a. Difficulties with thermodynamics calculations
b. Free energy perturbation method
7. Structure-Based Drug Design
a. Predicting protein-biomolecule structures
b. The search problem
c. Virtual screening
d. Conformational flexibility
The coursework requires some experience in programming. If you do not
have this experience, our course 'Introduction to software development
in Java' would be a suitable preparation.
You will find more information on these modules, and on all our other
courses here : http://octette.cs.man.ac.uk/bioinformatics/index.html If
you have any questions, or need advice on the module options, please
contact Heather.Vincent from manchester.ac.uk
