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Structural Biochemistry and Bioinformatics

Project for Structural Biochemistry and Bioinformatics

In this project you will be given a protein sequence. The task is to find as much information about the protein as possible by applying all the methods you have learned during the course.

You can get your sequence at http://www.sbc.su.se/~bjorn/kurser/struktbiokemi_2004/project.cgi, the password will be given to you at the project information. If you do not have the password you can mail me at bjorn@sbc.su.se.

It is a good idea to start working with your sequence as soon as possible and apply different methods in connection to the practical assignments. Tuesday 14/12 you should deliver one A4 page status report, containing what you have done sofar and what you plan to do.

These are steps that SHOULD be done and included in the presentation:

• Report about database searches
• Report about other prediction methods
• A homology model of the sequence. Describe what steps you have done to make the best possible model. Please note that it may not be possible to make a model of the whole sequence, but only for a part of it.
• Read an article about the protein that has been used as template for the homology model
• Read a paper (preferably a review) about your protein
• Evaluate the model from a structure-function perspective. Compare the active site (if there is one) between the template and the model. How high is the sequence identity? How good do you think your model is?

The project should be presented both as a paper (due 14/1) and as an oral presentation (16/1). The paper should contain at least 4 pages of text (and any amount of figures). It should be written in English and in the form of a short "scientific paper", i.e. it should include the following session: Abstract, Introduction, Methods, Results & Discusssions and Conclusions. If the paper is not delivered at this time you will not be allowed to give your oral presentation. The presentation should be for 15 minutes and include the most important findings.

You can choose to do the project alone or in a pairs, and a grade (U/G/VG) will be given and used together with the grade for the other parts to give you the grade of the whole course.

Important dates

1. 25/11 Project information
2. 14/12 Short presentation of project status. You should deliver one A4 page status report.
3. 11/1 Chance for help with project
4. 12/1 Project paper should be submitted.
5. 14/1 Project Presentation