Applied Pharmaceutical Structural Bioinformatics, 5 credits

Academic year 2021/2022

  • Autumn 2021, Mixed, 50%, Distance learning

    Start date: 30 August 2021

    End date: 14 October 2021

    Application deadline: 15 April 2021

    Application code: UU-37316 Application

    Language of instruction: English

    Location: Flexible

    Selection: All qualified applicants will be admitted.

    Outline for distance course: The course is given as audio-visual web-lectures, through down-loadable 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 e-mail. Written examination is performed online at the end of the course.

    Number of mandatory meetings: 0

    Number of voluntary meetings: 0

    Registration: 30 July 2021 – 13 September 2021

  • Spring 2022, Mixed, 50%, Distance learning

    Start date: 17 January 2022

    End date: 3 March 2022

    Application deadline: 15 October 2021

    Application code: UU-87316 Application

    Language of instruction: English

    Location: Flexible

    Selection: All qualified applicants will be admitted.

    Outline for distance course: The course is given as audio-visual web-lectures, through down-loadable 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 the students can carry out their duties at any time of each study week. Communication between teacher and students is via educational platform and via e-mail. Written examination is performed online at the end of the course.

    Number of mandatory meetings: 0

    Number of voluntary meetings: 0

    Registration: Please contact the department.

Entry requirements: 150 credits in chemistry, biology, biochemistry, pharmacy, medicine or dentistry; or other equivalent education under special review.

Fees:

If you are not a citizen of a European Union (EU) or European Economic Area (EEA) country, or Switzerland, you are required to pay application or tuition fees. Formal exchange students will be exempted from tuition fees, as well as the application fee. Read more about fees.

Application fee: SEK 900

Tuition fee, first semester: SEK 12,083

Tuition fee, total: SEK 12,083

About the course

The course teaches 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 data base 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.

More information

Contact

Department of Pharmaceutical Biosciences

Biomedicinskt centrum BMC, Husargatan 3

Box 591, 751 24 UPPSALA

Ola Spjuth

Email: ola.spjuth@farmbio.uu.se