Monash home  About Monash  Faculties  Campuses  Contact Monash 
Staff directory  AZ index  Site map 
(PHA)

Leader: Dr David Chalmers
Offered:
Parkville Second semester 2006 (Day)
Synopsis: An introduction to the techniques and applications of molecular modelling with particular emphasis on methods used in drug design: Concepts in computational chemistry. Introduction to quantum mechanics. Molecular mechanics. Optimization. Molecular simulation. Molecular modelling of water. Molecular structure. Drug design.
Objectives: At the completion of this unit the student will have:  A broad understanding of computational chemistry and its application to drug biomolecular problems.  An understanding of common molecular modelling terminology.  An appreciation of the factors involved in performing quantum mechanical (QM) calculations and the information that these calculations can provide.  An appreciation of molecular mechanisms energy calculations and the information that these calculations can provide.  An understanding of the components making up molecular mechanic force fields including bond stretching, angle bending and dihedral angle terms and nonbonded interactions (van der Waals and electrostatic).  An understanding of molecular potential energy surfaces and the concepts of global and local minima.  An appreciation of energy optimisation methods including steepest descents and conjugate gradient methods.  An appreciation of approaches to finding global energy minima.  An understanding of the Boltzmann distribution and the relationship between temperature and teh population of energetic states.  An appreciation of Monte Carlo methods.  An appreciation of Molecular Dynamics methods including molecular vibrations.  An appreciation of the physical properties of temperature and pressure; the principles of conservation of momentum and energy; how molecules behave when they collide.  An understanding of the importance of conformational flexibility in biomolecules including Ramachandran plots for proteins.  An understanding of the concept of a pharmacophore.  An appreciation of the applications of databases in drug development.  The ability to use a specific molecular modelling package to study molecular conformation and analyse drugreceptor interactions.
Assessment: Practical work / tests 30%; Examination 70%
Contact Hours: 12 weeks of 3 Lectures, 1 week of 1 Tutorial / 1 Lecture, and 9 x 4 hour Practicals.