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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!
O 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

O 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

O 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

O 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

O 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

O 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

O 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

O 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

O Wednesday, March 31

EASTER HOLIDAYS - No Class

O 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

O 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

O 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

O Wednesday, April 28

8.00-12.00
Group work on poster and oral presentations
Thomas Blicher

O Wednesday, May 5

8.00-12.00
Poster presentation and symposium
Course evaluation!

EXAM DATES - exam schedule to be announced later.

O Thursday, May 12

8.00-16.00
EXAM

O Wednesday, May 19

8.00-16.00
EXAM