[Molecular-modelling] Molecular Modelling and Structure-based Drug Design, March 2009

Heather Vincent via molmodel%40net.bio.net (by Heather.Vincent from manchester.ac.uk)
Tue Dec 30 17:37:32 EST 2008

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 

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

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