[MM] Molecular Modelling

This module will provide an introduction to the theory and practice of computer-based molecular modelling techniques such as molecular mechanics and dynamics, homology modeling and molecular docking that are becoming increasingly important to the practice of Structural Biology.

Lecturers

[toc]Dr Arvind Varsani (Electron Microscope Unit) has a Pharmaceutical Chemistry and Molecular Biology background. He will present lectures on various aspects of virus structures, assist in the electron microscopy module and provide molecular biology support for the programme. Dr Muhammed Sayed, Department of Biotechnology (UWC), is a protein crystallographer who completed his post-doctoral studies under Professor Tom Blundell at Cambridge University. He will supervise the web-courses in protein structure and protein crystallography. His goal is to develop protein crystallography as a practical discipline. Lecturers also include Kevin Naidoo, Michelle Kuttel and Colin Kenyon.

Top

Main Outcomes

The ability to:

understand the principles of molecular modeling and homology modelling,
use appropriate software to perform optimizations of molecular structures, run molecular dynamics calculations, perform normal mode analysis, create a homologous structure model from a know structure and perform molecular docking calculations.

This module descriptor document also can be downloaded as an MS-Word document.

Top

Main Content

Molecular Mechanics
Molecular Dynamics
Structure based sequence alignment
Homology modeling
Molecular docking

Home Department:	Computer Science (UCT)
Module description (Header):	Computational and Mathematical Primer
Generic module name:	Structural Biology
Alpha-numeric code:	STB705
Credit Value:	15 Credits
Duration:	6 Weeks
Module Type:	P
Level:	8
Prerequisites:
Co-requisites:	None
Prohibited combinations:	None
Learning time breakdown (hours):
Contact with lecturer/tutor:	60
Assignments & tasks:	40
Tests & examinations:	5
Practicals:	0
Selfstudy:	35
Total Learning Time	150
Methods of Student Assessment:	Weekly computer based tutorials will count approximately equally towards the final mark. Students will be required to make an oral presentation. Moderation will be internal.