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. |
The aims of this course are:
At the end of this course, students should:
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.
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.
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 |
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.
This course is arranged in cooperation with the following graduate education programmes: