Protein structures: production, prowess, power, promises, and problems (4th edition)


30 October – 3 November 2017 


  • Gert Vriend (CMBI, course coördinator)
  • Daniel Hoffmann (University Duisburg/Essen (TBC))
  • Hanka Venselaar (CMBI)
  • Bart van Beusekom (NKI)


Center for Molecular and Biomolecular Informatics (CMBI), Radboud University Nijmegen-Medical Centre /NCMLS, Nijmegen, the Netherlands

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. The course schedule accommodates both groups, parallel sessions for both groups will be scheduled when necessary.

NB: Some prior knowledge is needed. At the course webpages ( you fins a section called ‘Homework’ Please go through this part of the course (long) before you enter the course. If this homework is not easy for you, then you might ask yourself (or the course teachers) if this course will be good for you.

Study load

3 EC

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.

Examples of questions you will be able to answer after follwing 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?

Preliminary course schedule

Day 1: Homology modelling seminar (H Venselaar).

YASARA practicals

  • Watching and seeing protein structures
  • Homology modelling
  • Answering biological/biomedical questions using protein structures and models”.

Day 2: Protein structure comparison seminars (H Venselaar, G Vriend).


  • Sequences analysis when structure data is available
  • Answering medical questions with sequence-structure alignments

Day 3: Electrostatics and molecular dynamics seminars (D Hoffmann).


  • Role of electrostatics
  • Answering biological questions with MD

Day 4: Protein structure determination and validation seminars (Bart van Beusekom, G Vriend).


  • X-ray and NMR structure comparison
  • Protein structure validation and implications

Day 5: Own project executed with help from CMBI staff.

Travel & housing

Please check the following webpage for more information about travel information & hotels in the vicinity of the course venue.