Applied Structural Bioinformatics 6-9 September 2010


This applied course will give the participant pratical insight into modern tools for investigating protein structure and dynamics.


The course will give an introduction to visualization and investigation of 3D protein structures. PyMOL will be used for making figures for publications and presentations. Potential binding pockets and electrostatics properties of proteins will be covered, as well as structure prediction and homology modelling. The last part of the course will be dedicated to an introduction to normal modes analysis (NMA) and molecular dynamics (MD) simulations for the investigation of protein dynamics.

Duration: 3 full days with lectures and hands-on tutorials.

Optional: 4th day with possibility to apply newly acquired skills on your own project under guidance (possibly on your own laptop).

Brief content overview:

Visualization and investigation

  • PDB – Protein DataBase

  • PyMol

  • Figures for publications and presentations

Binding Pocket Predictor:

  • CastP and visualization in PyMol


  • Visualization in PyMol

Structure prediction and homology modelling

  • Expasy structure prediction

  • Expasy homology modelling

Protein dynamics

  • WebNMA

  • Amber

  • What can be learned with MD simulations

Open time

  • Investigate the structure and dynamics of your own protein.


Computational Biology Unit, Bergen, Høyteknologisenteret i Bergen (HiB).


The course is intended for PhD level and Post Doc level participants that have basic knowledge on protein structure from the fields of biology, molecular biology or biomedicine, and who want to get and introduction to computational tools for use in their research. A medium level of computer skills is required, as we will be using a combination of online tools, windows-based programs, and command-line based programs.


FUGE Bioinformatics Platform, Bergen Node, Computational Biology Unit, Uni BCCS.

Contact Person(s)

Lars Skjærven (lars.skjarven at

Kjell Petersen (kjell.petersen at

The course is free of charge. No meals are included, the course will take place next to the University canteen and there are other options nearby. Attendees in need of lodging will need to arrange this directly with a hotel in Bergen. Contact us for recommendations if needed.


Number of Seats



Registration Start
Registration End
Course Start
Sep. 6, 2010 9:00 am
Course End
Sep. 9, 2010 4:00 pm
Click here to go to Course Home Page