Structural Bioinformatics (TDA506)

2008/2009

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.

This course builds on the introductory material on Protein Structure that was given in period 1. Students should be familiar with that material.

News

2009-11-30	The January 2010 re-exam will be arranged by the Deperment of Computer Science and Engineering. Sign up for this exam by sending an e-mail message to Graham Kemp by 25 December 2009.
2009-03-26	The March 2009 exam paper and solutions are available (local access only).
2009-03-05	Please complete the on-line course evaluation form. The deadline for this is 23 March 2009. The password is available from Graham Kemp.
2009-02-16	The lecture at 10:00 on Monday 16 February is cancelled due to illness.
2009-02-04	Links to Assignments 1 and 2 have been added to the web site.

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.

Assessment

Grades will be determined by a written exam at the end of the course (08:30, 12 March 2009, V Building). But in order to pass the course you must also submit solutions to specified exercises.

The March 2006 exam paper and solutions are available (local access only).

Assignment	Date set	Date due
Assignment 1	4 February 2009	27 February 2009
Assignment 2	4 February 2009	27 February 2009
Assignment 3	3,5 March 2009	3,5 March 2009

There is an on-line list of students who have completed the practical work (local access).

Date	Time	Place	Activity
Monday 19 January	10:00-11:45	MVF23	Lecture (GK): Introduction; transformations and superposition
Tuesday 20 January	13:15-15:00	MVF25	Practical
Wednesday 21 January	10:00-11:45	MVF23	Lecture (GK) Protein domains
Friday 23 January	10:00-11:45	Pascal	Lecture (GK) Macromolecular structure determination by X-ray crystallography
Date	Time	Place	Activity
Monday 26 January	10:00-11:45	MVF23	Lecture (GK) Macromolecular structure determination by NMR spectroscopy
Tuesday 27 January	13:15-15:00	MVF25	Practical
Wednesday 28 January	10:00-11:45	MVF23	Lecture (GK) Sequence-structure relationships
Friday 30 January	10:00-11:45	Pascal	Lecture (GK) Comparative modelling
Date	Time	Place	Activity
Tuesday 3 February	13:15-15:00	MVF25	Practical
Wednesday 4 February	10:00-11:45	MVF23	Lecture (GK) Side-chain modelling
Friday 6 February	10:00-11:45	Pascal	Lecture (GK) Fold recognition; MHC-peptide interactions
Date	Time	Place	Activity
Monday 9 February	10:00-11:45	MVF23	Lecture (GK) Structural alignment
Friday 13 February	10:00-11:45	Pascal	Lecture (GK) New fold methods for protein modelling
Date	Time	Place	Activity
Monday 16 February	10:00-11:45	MVF23	Lecture - Cancelled
Tuesday 17 February	13:15-15:00	MVF25	Practical
Wednesday 18 February	10:00-11:45	MVF23	Lecture (GK) Protein surfaces and protein-protein docking
Friday 20 February	10:00-11:45	Pascal	Lecture (GK) Combinatorial docking and structural proteomics
Date	Time	Place	Activity
Monday 23 February	10:00-11:45	MVF23	Lecture (GK) Membrane proteins; channels
Tuesday 24 February	13:15-15:00	MVF25	Practical
Wednesday 25 February	10:00-11:45	MVF23	Lecture (GK) Protein design; antibody engineering
Friday 27 February	10:00-11:45	Pascal	Lecture (GK) RNA structure analysis and modelling
Date	Time	Place	Activity
Monday 2 March	10:00-11:45	MVF23	Lecture (PGN) Drug design - an overview; structure-based drug design
Tuesday 3 March	13:15-15:00	MVF25	Practical
Wednesday 4 March	10:00-11:45	MVF23	Lecture (PGN) Docking and structure-based drug design (SBDD)
Thursday 5 March	13:15-15:00	MVF25	Practical
Friday 6 March	10:00-11:45	Pascal	Lecture (PGN) Fragment and ligand-based drug design; cabohydrate structure and modelling

Practical exercises

Practical GK-1: Programming for structural bioinformatics (can be done before the first lecture)
Practical GK-2: Protein conformation (can be done before the first lecture)
Practical GK-3: Transformations and superposition (after lecture on 2009-01-19)
Practical GK-4: Protein domains (after lecture on 2009-01-21)
Practical GK-5: Structures determined by X-ray crystallography (after lecture on 2009-01-23)
Practical GK-6: Structures determined by NMR (after lecture on 2009-01-26)
Practical GK-7: Comparative modelling (after lecture on 2009-01-30)
Practical GK-8: Side-chain modelling (after lecture on 2009-02-04)
Practical GK-9: Structural alignment (after lecture on 2009-02-09)
Practical GK-10: Protein surfaces and protein-protein docking (after lecture on 2009-02-18)
Practical GK-11: Membrane proteins (after lecture on 2009-02-23)
Practical GK-12: Protein design (after lecture on 2008-02-25)
Practical GK-13: Antibody engineering (after lecture on 2008-02-25)
Practical PGN-1: Drug design
Practical PGN-2: In silico docking; Molecular databases for drug design

News

Aims

Objectives

Assessment

Personnel

Literature

Preliminary Schedule

Practical exercises