Applied Pharmaceutical Structural Bioinformatics

About the course

The course teaches you how to solve practical problems in pharmacology, life sciences and bioinformatics using free software and databases relating to the structure of functional proteins and drug targets.

The course covers bioinformatics for nucleotide and amino acid sequences and structural bioinformatics. This includes methods, databases and software for analysis and management of amino acid and nucleotide sequences, secondary and tertiary structures of proteins, methods and tools for homology modelling of protein 3D structure, and molecular dynamics simulations and molecular docking. The focus of the course is on practical exercises where you solve problems using your computer.

Specifically, the course contains the following sections:

• Introduction to Structural Bioinformatics in the pharmaceutical field.
• Alignment sequences and database searching. Practical exercises in pairwise and multiple sequence alignments, and exercises with sequence databases with applications in the pharmaceutical field.
• Techniques for prediction of secondary protein structure with computational tools and review of the Pfam and PROSITE databases.
• Techniques and methods for prediction of protein 3D structure: Background molecular modelling and energy minimisation. Tools for homology modelling of protein 3D structure and methods for validation of 3D structures.
• Practical exercises with the 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.

Outline for distance course: The course is given as audio-visual web-lectures, through downloadable documents for self-studies and teacher-supervised exercises online through a web-based teaching platform, and through exercises that students solve on their own computers using software that can be downloaded from the net. The course has no fixed times and students can carry out their duties at any time of each study week. Communication between teacher and students is via educational platform and via email. Written examination is performed online at the end of the course.