Graduate Course in
Structural Bioinformatics

11-15 December 2006


This is an intensive one-week PhD course.

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.

Beta-helix

Aims

The aims of this course are:

Objectives

At the end of this course, students should:

Course content

Protein, nucleic acid and carbohydrate conformation; levels of protein structure; secondary structure assignment, including DSSP; assessing stereochemical quality; factors affecting protein stability; structure classification hierarchies; three-dimensional structures of biological macromolecules; contact maps and distance maps; domain assignment; structure superposition; structure comparison; comparative protein modelling; protein fold recognition; Monte Carlo methods and simulated annealing; ab initio protein structure prediction; protein shape representation; protein-ligand interactions and applications in drug design; conformational analysis; protein-protein docking; modelling transmembrane proteins, carbohydrates and RNA; applications of structural bioinformatics.

Teacher

Graham Kemp

Course assignment

The course assignment is to write a popular science description based on one of Prof David Jones' research papers.

Students from the Chalmers Graduate School in Bioscience should complete the assignment after meeting David Jones in February 2007.

Schedule

Date Time Place Activity
Monday 11 December 2006 10:00-11:45 ES52 Lecture:
Protein structure
Monday 11 December 2006 13:15-15:00 6225 Practical:
Protein structure
Monday 11 December 2006 15:15-17:00 ES52 Lecture:
Protein domains
Date Time Place Activity
Tuesday 12 December 2006 10:00-11:45 ED Lecture:
Transformations, superpostion and structural alignment
Tuesday 12 December 2006 13:15-15:00 6225 Practical:
Protein structure and function
Tuesday 12 December 2006 15:15-17:00 EL42 Lecture:
Comparative modelling
Date Time Place Activity
Wednesday 13 December 2006 10:00-11:45 ES52 Lecture:
Fold recognition; MHC-peptide interactions; antibodies
Wednesday 13 December 2006 13:15-15:00 6225 Practical:
Comparative Modelling
Wednesday 13 December 2006 15:15-17:00 ES52 Lecture:
New fold methods for protein modelling
Date Time Place Activity
Thursday 14 December 2006 10:00-11:45 ES52 Lecture:
Molecular surfaces and protein-protein docking
Thursday 14 December 2006 13:15-15:00 6225 Practical:
Protein surfaces and protein-protein docking
Thursday 14 December 2006 15:15-17:00 ES52 Lecture:
Protein design; membrane proteins
Course ends

Venue

The course take place in the Department of Computer Science and Engineering at Rännvägen 6B on the main Chalmers campus.

The easiest way to find room ES52 is to enter the building at Rännvägen 6B, take the stairs (or lift) to level 5, walk straight ahead, down 3 steps and through the glass door, walk on for about 30 metres, then turn to the left. Room ES52 is one of the small lecture rooms inside the glass ``lens' ("Linsen"). in the centre of the building.

Research Schools

This course is arranged in cooperation with the following graduate education programmes: