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Åbo Akademi University 2014/2015
ÅBO CAMPUS
Biosciences
Biochemistry
Several courses are taught inEnglish throughout the academic
year, however not all courses are given every year. Prerequi-
sites for the classes: students should have at least two years of
prior studies in biochemistry and a good general knowledge
of chemistry.
It is also possible to do laboratory practice (7-15 weeks) in
different research groups. Prerequisites for laboratory prac-
tice: Students are in general required to be on the MSc-level.
A laboratory safety course at Åbo Akademi is also required
before a student canwork in a laboratory. Please consult Peter
Mattjus for more information about further prerequisites for
doing laboratory practice, which depends on the background
of the student.
Computers in Bioresearch
211009.0
2 credits
Basic level
Lectured course
Offered: Autumn 2014 (repeated during spring 2015 upon
request)
Lecturer: Tiina Salminen
Aim and content: The purpose of the course is to provide
the basic knowledge in computer science for beginners;
computers, Windows and Linux operating systems, and
computational terminology. The main focus is in the usage
of computers with the linux operating system including the
most important linux commands and tools needed during
structural bioinformatics courses. The course is given in the
Moodle e-learning platform.
Prerequisites: Basic knowledge in biochemistry. Sign-up in
advance electronically on site
/
coursesbiosci.
Target audience: Year 2 or 3
Form of assessment: Examination, Project reports
Contact hours: Introductory lecture, computer exercises,
projects
Course literature: All notes and materials provided. Cynthia
Gibas, Per Jambeck: Developing Bioinformatics Computer
Skills
Applied Bioinformatics
282005.0
6 credits
Intermediate level
Lectured course
Offered: Autumn 2014
Lecturer: Tiina Salminen
Aim and content: The purpose of the course is to give practi-
cal introduction to data, methods and computing important
to bioresearch today. The main focus is in the network based
tools and resources for molecular and structural biology.
Prerequisites: Basic knowledge in biochemistry. Sign-up in
advance electronically on site
/
coursesbiosci.
Target audience: Year 2 or 3
Form of assessment: Examination, Project reports
Contact hours: Lectures, computer exercises, projects
Course literature: All notes and materials provided. Recom-
mended literature Jin Xiong (2006) Essential bioinformatics
Protein structure in bioscience
4 credits
Intermediate level
Lectured course
Offered: Spring 2015
Lecturer: Tiina Salminen
Aimand content: Themain goal is to provide the student with
good knowledge on the three-dimensional (3D) structure of
proteins and the relationships between sequence, structure
and function. The course is based on published structures
and their usage in bioscience research, biotechnology and
drug design.
Prerequisites: Basic knowledge in biochemistry. Sign-up in
advance electronically on site
coursesbiosci.
Target audience: Year 2 or 3
Form of assessment: Examination, Project report
Contact hours: Lectures, computer exercises, projects
Course literature: All notes and materials provided.
Computer-aided drug design
4 credits
Advanced level
Lectured course
Offered: Spring 2015 (period 4)
Lecturer: Tiina Salminen
Aim and contents: This course gives an understanding of
how drugs interact with macromolecules and strategies for
how this information can be used in designing novel thera-
peutics using computational methods. The computational
strategies based on the 3D structures of small molecules are
also presented. The course contains lectures and computer
exercises on ligand-based and structure-based drug design,
drug-protein interactions, ligand docking, conformational
analysis, pharmacophore hypothesis and quantitative struc-
ture-activity relationship.
Prerequisites: Basic knowledge in biochemistry. Sign-up in
advance electronically on site
coursesbiosci.
Target audience: Year 4 or 5
Form of assessment: Examination, Project
Contact hours: Lectures (12h), computer exercises (8h), project
Course literature: All notes and materials provided. Hans-
Dieter Höltje, Wolfgang Sippl, Didier Rognan, andGerd Folkers
(2003) Molecular modeling: basic principles and applications.
Advanced studies in Structural Bioinformatics
13 credits
Advanced level
Supervised research work
Offered: Upon agreement during the academic year.
Lecturers: Mark Johnson and Tiina Salminen
Aims/contents: Advanced studies in structural bioinformatics
as part of a scientific research project
Prerequisites: Basic knowledge in biochemistry and an inter-
mediate/advanced level course in structural bioinformatics.
Target audience: Year 4 or 5
Form of assessment: Project report and oral presentation of
results.
Contact hours: Supervised research work in structural bioin-
formatics for eight weeks including report and presentation
of the work.
Course literature: All notes and materials provided.
