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Programme, Spring 2010
February 3 to May 5, 2010
Lectures and exercises will take place at
the Technical University of Denmark in Lyngby, Wednesdays from 8.00 to 12.00 in room 062, building 208.
Classes will be a mixture of lectures and group work. Part of the group work will consist of computer exercises
(borrow a portable from us or bring your own - requires wireless network and some software).
Please note:
the program may change slightly along the way.
The required readings for a class can be trusted from one week prior to the class.
The exact content of powerpoint slides and handouts may change up to the last minute!
 Wednesday, February 3
- 9.00-12.00 Notice the starting time!
- Introduction to the course and a general overview
- Introduction to Influenza
- Initializing groups for group work
Thomas Blicher
Wednesday, February 10
- 8.00-12.00
- Levels of protein structure, primary - quaternary structure
Thomas Blicher
- Reading assignment: B&T, chapters 1+2
- EXERCISE: Building a model of a protein structure by hand
Thomas Blicher, Thomas Nordahl Petersen, Irene Kouskoumvekaki and Olivier Taboureau
Wednesday, February 17
- 8.00-12.00
- Protein structures and structure visualization: Introduction to PDB & PyMOL
Thomas Blicher
- Reading assignment: B&T, chapters 3+4, two articles by Berman et al. describing the PDB
- EXERCISE: PDB and PyMOL tutorial
Thomas Blicher
Wednesday, February 24
- 8.00-12.00
- Experimental protein structure determination.
Thomas Blicher
- Reading assignment: B&T, chapter 6, p. 89-96 and p. 104-105
chapter 18, p. 373-384 and p.387-392
Structure article by Gajhede et al., Nature Stuctural Biology 1996
- EXERCISE: Structure article questions
Thomas Blicher
Wednesday, March 3
- 8.00-12.00
- Structure validation: Closest homologues and pathological cases
Anne Mølgaard
Reading assignment: "Structural Quality Assurance" by Roman Laskowski. Chapter 14 from Structural Bioinformatics by Bourne & Weissig. Copy available on CampusNet.
- EXERCISE: Model validation. LINK
Thomas Nordahl Petersen
Wednesday, March 10
- 8.00-12.00
- Prediction of local structural features: Secondary structure, surface accessibility and protein disorder
Thomas Blicher and Bent Petersen
Reading assignment: Paper by Ginalski et al., Nucleic Acid Research, 2005 - also see the reading guide.
Paper by Linding et al., Structure 2003 - also see the commentary by Iakoucheva & Dunker, Structure 2003.
- EXERCISE: Prediction from sequence. LINK
Thomas Blicher and Thomas Nordahl Petersen
Wednesday, March 17
- 8.00-12.00
- Homology modeling 1: Homology modeling and structural genomics
Thomas Blicher
Reading assignment: "Homology Modeling" by Elmar Kriger et al. Chapter 25 from Structural Bioinformatics by Bourne & Weissig. Copy available on CampusNet.
- EXERCISE: Homology modelling of hemagglutinin and neuraminidase
Thomas Blicher and Thomas Nordahl Petersen
Wednesday, March 24
- 8.00-12.00
- Homology modeling 2: Model refinement, force fields, difficult cases, ab initio
Thomas Blicher
Reading assignment:
- EXERCISE: Fold recognition - homology modelling with low homology
Thomas Blicher
Wednesday, March 31
- EASTER HOLIDAYS - No Class
Wednesday, April 7
- 8.00-12.00
- Protein structure analysis 1: Post-translational modifications, epitopes and variability
Thomas Blicher
Reading assignment:
- EXERCISE: PyMOL handin exercise I
Thomas Blicher
Wednesday, April 14
- 8.00-12.00
- Protein structure analysis 2: Case study - analyzing hemagglutinin and neuraminidase
Thomas Blicher
Reading assignment:
- EXERCISE: PyMOL handin exercise II
Thomas Blicher
Wednesday, April 21
- 8.00-12.00
- Protein engineering - how to modify the properties of proteins
Birte Svensson (EPC)
Reading assignment:
- EXERCISE: Start group work on projects
Thomas Blicher
Wednesday, April 28
- 8.00-12.00
- Group work on poster and oral presentations
Thomas Blicher
Wednesday, May 5
- 8.00-12.00
- Poster presentation and symposium
- Course evaluation!
Thursday, May 12
- 8.00-16.00
- EXAM
Wednesday, May 19
- 8.00-16.00
- EXAM
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