Faculty of Pharmacy and Pharmaceutical Sciences

Monash University

Undergraduate - Unit

This unit entry is for students who completed this unit in 2015 only. For students planning to study the unit, please refer to the unit indexes in the the current edition of the Handbook. If you have any queries contact the managing faculty for your course or area of study.

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6 points, SCA Band 2, 0.125 EFTSL

Refer to the specific census and withdrawal dates for the semester(s) in which this unit is offered.

FacultyFaculty of Pharmacy and Pharmaceutical Sciences
OfferedParkville Second semester 2015 (Day)
Coordinator(s)Dr David Chalmers


Previously coded PSC2141


This unit provides an introduction to the techniques and applications of molecular modelling with particular emphasis on methods used in drug design.

The unit contains two streams:

  1. modelling methods; which introduces quantum mechanics, molecular mechanics, energy optimisation and molecular simulation and
  2. modelling applications; which covers quantitative structure-activity relationships (QSAR), pharmacophores, structure-based drug design and homology modelling.

This will involve:

  • modelling methods in computational chemistry
  • applications of molecular modelling


At the end of this unit students will have:

  1. A broad understanding of computational chemistry and its application to drug bimolecular problems;
  2. 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;
  3. An appreciation of molecular mechanisms energy calculations and the information that these calculations can provide;
  4. 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);
  5. An understanding of molecular potential energy surfaces and the concepts of global and local minima;
  6. An appreciation of energy optimisation methods including steepest descents and conjugate gradient methods;
  7. An appreciation of approaches to finding global energy minima;
  8. An understanding of the Boltzmann distribution and the relationship between temperature and the population of energetic states;
  9. An appreciation of molecular simulation methods;
  10. An understanding of drug physicochemical properties including electronic, steric and hydrophobic characteristics;
  11. An understanding of the statistical methods used to develop QSAR equations;
  12. An appreciation of the application of QSAR in drug discovery;
  13. An appreciation of impact of drug physicochemical parameters on biopharmaceutical properties;
  14. An understanding of the pharmacophore concept and its use in drug discovery;
  15. An appreciation of structure and ligand-based drug design;
  16. An appreciation of homology modelling methods;
  17. The ability to use a specific molecular modelling package to study molecular conformation and analyse drug-receptor interactions;
  18. Describe the molecular interactions which govern molecular structure including bonded, non-bonded and electrostatic interactions.

After completing this unit the student will have the following practical skills:

  1. Perform simple molecular modeling studies using the molecular modeling package;
  2. Describe the processes involved in molecular mechanics energy calculations;
  3. Explain the processes involved in running quantum mechanics calculations;
  4. Interpret and critique a QSAR equation;
  5. Generate statistically acceptable QSAR equations from physicochemical parameters and biological activity data;
  6. Derive simple pharmacophore models;
  7. Describe protein-ligand interactions and how an understanding of these can be applied to drug design;
  8. Investigate a research topic using literature sources and write a simple report.


Final exam (2 hour): 60%; mid-semester exam: 20%; practical assessment: 20%.

Workload requirements

Contact hours for on-campus students:

  • Thirty six hours of lectures
  • Nine 4-hour practical classes

See also Unit timetable information

Chief examiner(s)


Additional information on this unit is available from the faculty at: