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[Molecular-modelling] Molecular Modelling and Structure-based Drug Design - deadline reminder

Heather Vincent via molmodel%40net.bio.net (by Heather.Vincent from manchester.ac.uk)
Mon Feb 2 16:31:30 EST 2009


This is a reminder for those people considering taking our online
course, which begins again in March 2009.

The application deadline is 13 February.  However, it is advisable to
apply before the deadline to allow time for any questions in processing
your application.

I have included the course outline below; the full details are on our
website
(http://octette.cs.man.ac.uk/bioinformatics/modules/bs6251.html).  If
you have any questions, or need advice on the module options, please
contact Heather.Vincent from manchester.ac.uk

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' 
(http://octette.cs.man.ac.uk/bioinformatics/modules/bs6250.html) would 
be a suitable preparation.



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