Faculty of Pharmacy and Pharmaceutical Sciences

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Monash University

Monash University Handbook 2010 Undergraduate - Unit

6 points, SCA Band 0 (NATIONAL PRIORITY), 0.125 EFTSL

FacultyFaculty of Pharmacy and Pharmaceutical Sciences
OfferedParkville Second semester 2010 (Day)
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 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, bioassays and screening methods. Pharmacophore generation and pharmacophoric groups in conjunction with subsequent database searching methods.

  • 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.

  • QSAR
Similarity, the QSAR module will discuss a range of methods and the underlying statistics and methodology. The following topics will be explored:
Classical QSAR, 2D, 2.5D and 3D methods, CoMFA, QSAR and the relationship to pharmacophores, fingerprint descriptors, linear and non-linear correlation methods, chance correlations, virtual databases, combinatorial chemistry and screening.


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

  1. Describe and explain the concept of druglikeness.
  2. Explain the importance of understanding molecular physicochemical properties in drug design.
  3. Outline the utility of databases in drug development.
  4. Detail the application of virtual screening in lead identification.
  5. Describe the application of pharmacophores for the selection of screening candidates.
  6. Describe and have a knowledge of basic methods in bioinformatics.
  7. Understand the application of advanced QSAR methods to drug discovery.
  8. Undertake projects that require researching information sourcesand 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 nine 3 hour practicals


VPS2141 Computational chemistry
VPS2062 Pharmacology

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