Applied Pharmaceutical Structural Bioinformatics

The course teaches how to solve practical problems in the areas of pharmacy and life sciences using structure based methods. If your interest is chemistry, including medicinal chemistry, you will also benefit from the course.

The focus is on practical work, where you conduct exercises and solve problems using freely available computer programs and databases.

The course covers databases and software for analysis of amino acid and nucleotide sequences, secondary and tertiary structure of proteins, methods and tools for homology modeling of protein 3D structure, molecular dynamics simulations and molecular docking,

This includes specifically:

  • Introduction to Structural Bioinformatics in the pharmaceutical field.
  • Sequence alignments and searches with practical exercises in pair and multiple sequence alignments, including work on sequence databases.
  • Techniques and software for prediction of protein secondary structure, including the Pfam and PROSITE databases.
  • Techniques and methods for prediction of protein 3D structure: background, molecular modeling and energy minimization. Tools for homology modeling of protein 3D structure. Validation of 3D structures.
  • Practical exercises with MODELLER software and structure validation with PROCHECK.
  • The physical basis for molecular dynamic simulation.
  • Exercises on molecular dynamic simulations of proteins with Gromacs.
  • Molecular docking and drug screening. Tools and applications relating to computer-aided drug design.
  • Practical exercises with Autodock and Autodock Vina tools.

Eligibility: At least 150 ECTS credits in chemistry, biology, biochemistry, pharmacy, medicine or dentistry.

Teaching: On the internet via a web-based teaching platform.

Language: English.

Examination: Written examination at the end of the course and approved compulsory modules.

Credits: 5 ECTS credits is given on passing the course.

Course literature: Provided online with the course and freely available computer programs that can be downloaded from the web and installed on your own computer.

Course starts: The course is given twice a year, each course running over eight weeks. The next course starts August 29, 2016.

Signing up: To sign up click here . (Important: When you sign up, please state in the message field that you are signing up for the course Applied Pharmaceutical Structural Bioinformatics).