Bioinformatics for protein sequence, structure and function

To read during Protein Structure (W44-48).

Additional necessary material is available from the web. if you click on the text link.

It is expected that you will spend about 1 day (8 hours) to complete one week of work. I guess the best is to spend the first 6 hours reading and the next 1 h 55 to do the assignments. The last 5 minutes hould be needed to fill in the answers.

Here is a list of people who passed the first assignments and Here the last assignments.

W 44 Signals in proteins and alignments of proteins.
- Introduction
- Sequence alignments
- Biological motivation
- Pairwise alignments
- Substitution matrixes
- signals.html How to detect and use sequence signals
1. Excercises: Predictions of signal sequences..
2. Excercises: How do I detect a pattern in a protein
3. Excercises: Logo creations. To do this it is necessary that you can view/print postscript files. Descriptions how this can be dne is available here
4. Excercises: How do I align two proteins.
W 45 Secondary structure predictions and membrane predictions.
- secstr.html Secondary structure predictions
- Membrane proteins
- Membrane protein structures
1. Excercises: Can I predict the secondary structure of a protein?
2. Excercises: Can I predict what part of a protein is in a membrane?
W 46 Threading and protein families.
- Multiple sequence alignments
- threading.html Threading - protein fold recognition

W 47 Homology modelling and verification of structures.

Arne Elofsson

Last modified: Wed Dec 13 17:25:13 CET 2000

Arne Elofsson Stockholm Bioinformatics Center, Department of Biochemistry, Arrheniuslaboratoriet Stockholms Universitet 10691 Stockholm, Sweden	Tel: +46-(0)8/161553 Fax: +46-(0)8/158057 Hem: +46-(0)8/6413158 Email: arne@sbc.su.se WWW: /~arne/