Graduate Course in
Structural Bioinformatics

23-26 September 2008


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

Preliminary Schedule

Date Time Place Activity
Tuesday 23 September 2008 10:15-11:00 6128 Lecture:
Protein structure
Tuesday 23 September 2008 11:00-12:00 6128 Lecture:
Protein structure classification
Tuesday 23 September 2008 13:15-15:00 6128 Practical:
Protein structure
Tuesday 23 September 2008 15:30-16:45 6128 Lecture:
Macromolecular structure determination
Date Time Place Activity
Wednesday 24 September 2008 09:00-09:45 6128 Lecture:
Transformations, superpostion and structural alignment
Wednesday 24 September 2008 10:00-11:45 6128 Practical:
Protein structure and function
Wednesday 24 September 2008 13:15-15:00 6128 Lecture:
Comparative modelling; fold recognition
Wednesday 24 September 2008 15:15-17:00 6128 Practical:
Comparative modelling
Date Time Place Activity
Thursday 25 September 2008 09:15-10:30 6128 Lecture:
New fold methods for protein modelling
Thursday 25 September 2008 10:45-11:45 6128 Lecture:
Molecular surfaces and protein-protein docking
Thursday 25 September 2008 13:15-14:30 6128 Practical:
Molecular surfaces and protein-protein docking
Thursday 25 September 2008 15:00-16:00 4128 Lecture:
Protein design
Date Time Place Activity
Friday 26 September 2008 09:00-10:00 6128 Lecture:
Membrane proteins
Friday 26 September 2008 10:00-11:45 6128 Practical:
Membrane proteins
Friday 26 September 2008 14:00-14:30 6128 Lecture:
MHC-peptide interactions
Friday 26 September 2008 14:30-16:00 6128 Discussion about practical work
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 6128 is to enter the building at Rännvägen 6B, take the stairs (or lift) to level 6, then through the glass doors, and room 6128 is on your right (behind the room with the photocopier).

Research Schools

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