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NBIC PhD course – Protein Structures: production, prowess, power, promises, and problems

4th November 2013 - 8th November 2013


NBIC PhD School
This course is part of the Education Programme of the NBIC PhD School. The NBIC PhD School offers training and education for PhD students in bioinformatics.

Target audience
The course is suitable for both PhD students working in structural bioinformatics as well as for PhD students in the life sciences who want to learn more about using structural informatioin in their research.

Course Description
In the right hands, protein structures are a ‘power’ful tool to answer bio-molecular questions. Knowledge of the structure is a pre-requisite for rational drug design, for biotechnology, for chemical biology, and for answering a whole series of biomedical questions. In this course we will discuss the ‘production’ of protein structures by NMR, X-ray, and homology modelling. These methods all have their pro’s and cons so a certain ‘prowess’ is needed to follow all ‘promises’ and start attacking bio-medical ‘problems’ using protein structures.

The course will be split in three parts.
Part 1) Looking and seeing things in protein structures, learning to operate the software, understanding some of the algorithms.
Part 2) Protein structure determination (prediction) with NMR, X-ray, and homology modelling, and the possibilities and problems that come with each of these three techniques.
Part 3) Applying all that was learned in real-life example studies.

Course topics
Day 1: Homology modelling
Day 2: Protein structure determination and validation
Day 3: Electrostatics and molecular dynamics
Day 4: Protein structure comparison
Day 5: Own project executed with help from CMBI staff.

Examples of questions you will be able to answer after following the course:

• Why is a person with this mutation sick? Or in other words, how does the molecular phenotype cause a disease state?

• This enzyme converts mannose. Can I make is specificity broader?

• This enzyme doesn’t function in my in vitro assay. Should I add some ions?

• I want to add a tag to my enzyme, should I put it on the N-terminus, the C-terminus, or is something different needed?

• This receptor binds a ligand, but if I look at the structure, that ligand doesn’t fit at all. Can I predict motions that take place upon ligand binding?

Course coordinator: Gert Vriend


4th November 2013
8th November 2013
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