6 points, SCA Band 2, 0.125 EFTSL
Undergraduate - Unit
Refer to the specific census and withdrawal dates for the semester(s) in which this unit is offered.
- Second semester 2018 (On-campus)
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:
- modelling methods; which introduces quantum mechanics, molecular mechanics, energy optimisation and molecular simulation and
- 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:
- A broad understanding of computational chemistry and its application to drug bimolecular 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 the population of energetic states;
- An appreciation of molecular simulation methods;
- An understanding of drug physicochemical properties including electronic, steric and hydrophobic characteristics;
- An understanding of the statistical methods used to develop QSAR equations;
- An appreciation of the application of QSAR in drug discovery;
- An appreciation of impact of drug physicochemical parameters on biopharmaceutical properties;
- An understanding of the pharmacophore concept and its use in drug discovery;
- An appreciation of structure and ligand-based drug design;
- An appreciation of homology modelling methods;
- The ability to use a specific molecular modelling package to study molecular conformation and analyse drug-receptor interactions;
- 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:
- Perform simple molecular modeling studies using the molecular modeling package;
- Describe the processes involved in molecular mechanics energy calculations;
- Explain the processes involved in running quantum mechanics calculations;
- Interpret and critique a QSAR equation;
- Generate statistically acceptable QSAR equations from physicochemical parameters and biological activity data;
- Derive simple pharmacophore models;
- Describe protein-ligand interactions and how an understanding of these can be applied to drug design;
- Investigate a research topic using literature sources and write a simple report.
Final exam (2 hour): 60%; mid-semester exam: 20%; practical assessment: 20%.
Contact hours for on-campus students:
- Thirty six hours of lectures
- Nine 4-hour practical classes
See also Unit timetable information