Graham Kemp > Teaching > Bioinformatics III |
This course, Bioinformatics III, is part of the International Master's Programme in Bioinformatics.
This course builds on the introductory material on Protein Structure that was given as part of Bioinformatics I. Students should review the contents of those lectures.
2005-03-07 | Assignment 4 is now available. |
2005-02-22 | A list of assignments received is available on-line. |
2005-01-28 | A bug in function tf_ptspts() resulted in the function sometimes returning an incorrect transformation matrix. I've fixed that bug and I've recompiled the transformation library. If the superpositions that you obtained in practical GK-2 were not good as you thought they should have been, please try running your program again. |
At the end of this course, students should:
This course will be assessed through a series of assignments.
Assignment | Weight | Date set | Date due |
Assignment 1 (GK) | 15% | 1 February 2005 | 21 February 2005 |
Assignment 2 (GK) | 25% | 7 February 2005 | 7 March 2005 |
Assignment 3 (GK) | 25% | 10 February 2005 | 22 February 2005 |
Assignment 4 (PGN) | 25% | 7 March 2005 | 18 March 2005 |
Assignment 5 (GK) | 10% | 3 March 2005 | 14 March 2005 |
Marks for the five assignments will be combined to give an overall grade for the course. Grade limits are: 50% for grade 3, 65% for grade 4, 80% for grade 5.
An individual lab account has been created for each student taking this course.
There are eight weeks in Quarter 3 this year, rather than the usual seven. However, we do not intend having more than 14 lectures.
There will be no lecture on Tuesday 8 February since this is one of the CHARM days. Related to Bioinformatics, you are welcome to attend the Genomics and Bioinformatics Open Day on Tuesday 8 February.
Date | Time | Place | Activity |
Tuesday 18 January | 13:15-15:00 | ES51 | Lecture (GK): Protein structure and function; domains |
Tuesday 18 January | 15:15-17:00 | ED6225 | Practical (GK): Protein structure and function; domains |
Thursday 20 January | 10:00-11:45 | ES53 | Lecture: Cancelled |
Thursday 20 January | 15:15-17:00 | ED6225 | Practical (GK): Protein structure and function; domains |
Date | Time | Place | Activity |
Tuesday 25 January | 13:15-15:00 | ES51 | Lecture (GK): Transformations and superpostion |
Tuesday 25 January | 15:15-17:00 | ED6225 | Practical (GK): Transformations and superpostion |
Thursday 27 January | 10:00-11:45 | ES53 | Lecture (GK): Comparative modelling |
Thursday 27 January | 15:15-17:00 | ED6225 | Practical (GK): Comparative modelling |
Date | Time | Place | Activity |
Tuesday 1 February | 13:15-15:00 | ES51 | Lecture (GK): Structure comparison; fold recognition |
Tuesday 1 February | 15:15-17:00 | ED6225 | Practical |
Thursday 3 February | 10:00-11:45 | ES53 | Lecture (PGN): Drug design |
Thursday 3 February | 15:15-17:00 | ED6225 | Practical (PGN) |
Date | Time | Place | Activity |
Thursday 10 February | 10:00-11:45 | ES53 | Lecture (GK): Ab initio protein modelling |
Thursday 10 February | 15:15-17:00 | ED6225 | Practical |
Date | Time | Place | Activity |
Tuesday 15 February | 13:15-15:00 | ES51 | Lecture (GK): Protein surfaces and protein-protein docking |
Tuesday 15 February | 15:15-17:00 | ED6225 | Practical (GK): Protein surfaces and protein-protein docking |
Thursday 17 February | 10:00-11:45 | ES53 | Lecture (PGN): Ligand conformation - force field methods |
Thursday 17 February | 15:15-17:00 | ED6225 | Practical (PGN) |
Date | Time | Place | Activity |
Tuesday 22 February | 13:15-15:00 | ES51 | Lecture (PGN): Oligosaccaride structure and modelling |
Tuesday 22 February | 15:15-17:00 | Room 2304, Medicinaregatan 7B | Practical (PGN) |
Thursday 24 February | 10:00-11:45 | ES53 | Lecture (AS): Macromolecular structure determination by X-ray crystallography |
Thursday 24 February | 15:15-17:00 | ED6225 | Practical (AS) |
Date | Time | Place | Activity |
Tuesday 1 March | 13:15-15:00 | Swedish NMR Center1 | Lecture (VO): NMR in biology |
Tuesday 1 March | 15:15-17:00 | Swedish NMR Center | Visit to Swedish NMR Center |
Thursday 3 March | 10:00-11:45 | ES53 | Lecture (GK): Antibodies; MHC-peptide interactions; protein structure databases |
Thursday 3 March | 15:15-17:00 | ED6225 | Practical (GK): Antibodies |
Date | Time | Place | Activity |
Tuesday 8 March | 13:15-15:00 | ES51 | Lecture (GK): Membrane proteins; Masters projects (1) |
Tuesday 8 March | 15:15-17:00 | ED6225 | Practical (GK): Membrane proteins |
Thursday 10 March | 10:00-11:45 | ES53 | Lecture (GK): RNA structure analysis and modelling; Masters projects (2) |
Thursday 10 March | 15:15-17:00 | ED6225 | Practical |
1 The Swedish NMR Center is at Medicinaregatan 5C (building "2").