Faculty of Pharmacy and Pharmaceutical Sciences

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Monash University

Monash University Handbook 2011 Undergraduate - Unit

6 points, SCA Band 0 (NATIONAL PRIORITY), 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
OfferedNot offered in 2011
Coordinator(s)Dr David Manallack


The Computational Chemistry II unit will focus on computational chemistry techniques in conjunction with related disciplines to provide a fundamental background to the field of drug design and drug discovery. The subject will cover a range of topics in the area of drug lead identification: structure based design, pharmacophores, molecular properties and databases, an introduction to bioinformatics and a short synopsis of advanced Quantitative Structure-Activity Relationships (QSAR) methods.

This will involve the study of:

  • Pharmacophores/databases
Within the topic of "pharmacophores/molecular properties and databases" the following topics will be explored: Representations of molecular and biological data, molecular and biological databases, prediction of molecular properties, the concept of 'druglikeness', prediction of bioavailability, Lipinski's rule of five and related studies, bioassays and screening methods. Pharmacophore generation and pharmacophoric groups in conjunction with subsequent database searching methods will also be explored.

  • Structure-based drug design
Within the topic of "structure-based drug design" the following topics will be explored":
docking, conformational and orientational searching (posing) and scoring methods. Applications of Structure-based drug design: virtual screening and de novo drug design.

  • Bioinformatics
The bioinformatics module will expose students to practical methods and the underlying algorithms used in contemporary software systems. Sequence alignment, BLAST searching and homology modelling will be covered.


At the end of this unit students will be able to:

  1. Describe and explain the concept of druglikeness.
  2. Analyze and explain the importance of understanding molecular physicochemical properties in drug design.
  3. Outline the utility of databases in drug development.
  4. Apply molecular fingerprint methods to assessing molecular similarity
  5. Detail the application of virtual screening in lead identification.
  6. Describe the application of pharmacophores for the selection of screening candidates.
  7. Describe and apply basic methods in bioinformatics.
  8. Undertake projects that require researching information sources and to present the findings in a structured, logical and fluent manner.
  9. Conduct and be proficient in chemical laboratory techniques, and communicating the results in written form.


Final exam (2 hour): 70%; Workshop/practical exercises and assignments: 30%.

Chief examiner(s)

Dr David Manallack

Contact hours

36 1 hour lectures and four 3 hour practicals


PSC2141 Computational chemistry

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