Applied Pharmaceutical Structural Bioinformatics 2020/2021 (5 credits)
Autumn 2020, Mixed, 50 %, Distance learning
Start date: 31 August 2020
End date: 15 October 2020
Application Deadline: 15 April 2020
Enrolment 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.
Spring 2021, Mixed, 50 %, Distance learning
Start date: 18 January 2021
End date: 4 March 2021
Application Deadline: 15 October 2020
Enrolment 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.
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 12083
Tuition fee, total: SEK 12083
About the course:
The course on Applied Pharmaceutical Structural Bioinformatics 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
E-mail: ola.spjuth@farmbio.uu.se