wins.
Dear students, welcome at the SFB course. This course deals with a large series op topics related to the structure, function, and bioinformatics of biomolecules, and with a strong focus on proteins. The course will consist of all material listed under SFB in the top-left window. The course will end with a report on a protein engineering task, and, of course the exam.
Your final grade for this course will be calculated as follows:
Participation from 9:15-17:15 is obligatory. One day missing will be forgiven. Two days missing will mean that you get an extra project. And three days missing will mean that we see you again next year (or not). We run a tight ship. Each year we loose a few people along the way, but so far everybody who worked hard during the course has passed SFB without 'hertentamen'; and we intend to keep it that way. If we feel that somebody is falling behind, then he or she will get homework and extra lessons.
The work-load is such that you
can always be ready with all work at 17:15. But only if you work hard.
Not when the lure of
wins.
Gert Vriend especially hates it when people start Emailing during his seminars.
We know it will be hard for you around the last two weeks of the course because the SFB project clashes with other courses in this same period, so please plan your work well.
You can all "rent" a USB stick. You pay 20 Euro for it. If you
return the USB stick at the end of the course, you get your money back. If you
don't return it, we earn 
12.05
but nevertheless will get a bad mood. You
can probably copy the full content on a private USB stick. The YASARA on this
stick will work on all computers in the Radboud network, even on computers
in the student flats.
This stick contains the extensive version of YASARA. This version is called Twinset and it contains WHAT IF. We will explain interactively how you work with this version. The memory stick also contains a version of YASARA-view that you can install on any computer anywhere. Some of you might be able to use the full Twinset version at home, but that will not be needed for the successful completion of this course.
In the Bioinformatics 1 course, known to you as either "Bioinformatics A", "Introduction to Bioinformatics", or the "Bioinformatics Seminar Series" you learned about the characteristics of amino acids, and the relation between these characteristics and protein structure. Take a quick look again at the amino acids and their characteristics before starting this course. Just as in Bioinformatics 1, this course is all about reading, thinking and understanding.
The material of Bioinformatics 1 is considered 'known'. Especially the part about the amino acids. Take a quick look at that course to get your amino acid knowledge refreshed. We will start the present course with a recap of the amino acids (which is new for the students who followed the Bioinformatics Seminar Series as Bioinformatics 1).
If you feel uncertain about your amino acid knowledge, feel free to test yourself. You can also try to play www.wiley.com/legacy/college/boyer/0470003790/animations/acideroids/acideroids.htm acideroids.
The book by Branden and Tooze is adviced (but not required) as it contains many chapters that go well with SFB, especially with aspects of the middle part of this course. Don't buy this book because it is very expensive, but the CMBI bought copies that you can borrow.
|
Figure 1. We will be using the book PROTEIN PHYSICS A course of lectures by Finkelstein and Ptitsyn, but only as background material. Going through the chapters indicated in the table in the next section is adviced to people who see their future in bioinformatics. |
It is very well possible to happily go through SFB without ever opening this book. If there are things you don't understand, though, it might help getting it explained in a very different way.
(Sorry, this is a bit in Dutch, obligatory for our in-house teaching)
In het eerste gedeelte van de cursus worden vouwings motieven en folds besproken. Hierna komen de details van macromoleculaire structuur aspecten aan de orde, en manieren om deze in silico aan te pakken. Deze kennis zal op haar beurt gebruikt worden voor de studie van structurele aspecten van belangrijke biomoleculaire processen, zoals transcriptie, transmembraan signaal-transductie, en transport en mobiliteit.
In het tweede gedeelte worden meer theoretische aspecten behandeld, zoals vouwing en stabiliteit, binding en thermodynamische aspecten van biomoleculaire interacties. De nadruk zal liggen op bioinformatische methoden die gebruikt worden bij voorspelling van topologieen, effecten van (punt-)mutaties en het ontwerp van experimenten gericht op biologische, biomedische, biotechnologische, en farmacologische onderwerpen.
Tussententamens, schriftelijk eindtentamen en een verslag over de eindopdracht. Aktieve deelname en participatie tellen mee in de beoordeling.
Er is geen verplichte literatuur.
Handouts zullen tijdens de cursus dagelijks uitgedeeld worden.