Structural Bioinformatics (2011/2012)

Structural Bioinformatics (2011/2012)

In this course we consider "structural bioinformatics" to be the development and application of computational methods (i) to analyse and predict the conformations of biological macromolecules and (ii) to study relationships between macromolecular structure and function. Protein molecules will be in focus, but other biological molecules will also be studied.

Why is this course relevant for Computing Science students?

Polyhedral protein surface representation

News

2012-02-09 Examination sign-up deadline is 2012-02-17.
2012-02-09 The second Assignment is online - see the link below.
2012-02-02 Today's lecture is cancelled. The first Assignment is online - see the link below.
2012-01-18 The next lecture will be in room ES62 at 15:15 on Thursday 19 January. There is a fully revised schedule in TimeEdit. Please note that the classes scheduled for 13:15-15:00 on Mondays will actually be lab classes in room MVF25.
2012-01-18 I hope to have updated schedule details on this web later today. Please check this evening or tomorrow morning.
2012-01-18 There will not be a lecture on Wednesday 18 January. However, I will be in computer lab MVF25 in the Mathematical Sciences Building betwen 15:15 and 17:00 (with another Bioinformatics class). If you would like to do some work on the TDA506 practicals at that time, you are welcome to join me in room MVF25 this afternoon, and I should have time to take any questions you might have regarding those practical exercises. The next TDA506 lectures will be on Thursday at 10:00 and Friday at 15:15, as shown in TimeEdit.
2012-01-15 The first lecture in this course is at 13:15 on Monday 16 January in room ES53. It will probably be necessary to make several changes to the timetable currently shown in TimeEdit - more information about this on Monday.

General Information

Aims

The aims of this course are:

  • to present some of the computational challenges in structural biology;
  • to describe computational methods for analysing and predicting macromolecular conformations and interactions;
  • to give practice in programming techniques for structural bioinformatics;
  • to give practice in the use of molecular graphics and modelling software;
  • to emphasise the relationship between macromolecular shape and function.

Objectives

At the end of this course, students should:

  • be familiar with algorithms and data collections that are central to structural bioinformatics;
  • understand computational methods used in protein modelling, docking, and other areas of structural bioinformatics;
  • be able to write programs to analyse protein structure data;
  • be able to use software packages for macromolecular structure analysis, modelling and docking;
  • be aware of applications of structural bioinformatics that are directed towards understanding and predicting biological function.
Ligand binding site prediction

Assessment

Grades will be determined by a written exam at the end of the course. But in order to pass the course you must also submit solutions to specified exercises.

AssignmentDate setDate due
Assignment 1 2 February 2012 24 February 2012
Assignment 2 9 February 2012 27 February 2012

Personnel


Last Modified: 24 February 2012 by Graham Kemp