• Basic information
• Learning outcomes
• Contents
• Assessment
• Workload

Learning outcomes

Upon successful completion of this course, students will be able to:

1. Perform comparisons of protein and DNA sequences

   Contribution to Program Outcomes

   1. Develop their knowledge in the fields of Bioengineering and Biotechnology at the level of expertise based on undergraduate qualifications.
   2. Define, model and solve engineering problems in the field of bioengineering at a higher level.
   3. Construct an experiment for a problem in the field of Bioengineering and Biotechnology, develop a solution method, solve it, evaluate the results and to have synthesis skills.

   Method of assessment

   1. Written exam
   2. Homework assignment
2. Utilize biological databases for bioengineering applications

   Contribution to Program Outcomes

   1. Use up-to-date techniques and computational tools for advanced engineering applications.
   2. Solve problems that require expertise in the field of bioengineering by using scientific research methods.

   Method of assessment

   1. Written exam
   2. Homework assignment
3. Prediction protein structures

   Contribution to Program Outcomes

   1. Define, model and solve engineering problems in the field of bioengineering at a higher level.
   2. Use up-to-date techniques and computational tools for advanced engineering applications.
   3. Solve problems that require expertise in the field of bioengineering by using scientific research methods.

   Method of assessment

   1. Written exam
   2. Homework assignment

Contents
Week 1:	Basic molecular biology for bioinformatics: gene and protein expression, cell metabolism and structure.
Week 2:	Primary biological databases
Week 3:	Secondary biological databases Homework I
Week 4:	Pairwise sequence comparisons: scoring matrices, global and local sequence alignment
Week 5:	Global sequence alignment Homework II
Week 6:	Local sequence alignment
Week 7:	Detection of homologous proteins from biological databases via local sequence alignment Homework III
Week 8:	Multiple sequence alingment and sequence conservation profiles
Week 9:	Sequence, structure, and function relationships in proteins
Week 10:	Protein structure analyses and structural bioinformatics
Week 11:	Computational protein design Homework IV
Week 12:	Structure-based drug discovery
Week 13:	Protein dynamics
Week 14:	Coarse-grained and atomistic protein dynamics simulations
Week 15*:	-
Week 16*:	Final exam
Textbooks and materials:	P. Selzer, RJ. Malhöfer, O. Koch, "Applied Bioinformatics", Springer Cham., 2nd Ed., 2018
Recommended readings:	J. Pevsner, "Bioinformatics and Functional Genomics", 3rd Ed., 2015
	* Between 15th and 16th weeks is there a free week for students to prepare for final exam.

Assessment
Method of assessment	Week number	Weight (%)
Mid-terms:		0
Other in-term studies:		0
Project:		0
Homework:	3, 5, 7, 11, 14	50
Quiz:		0
Final exam:	16	50
	Total weight:	(%)

Workload
Activity	Duration (Hours per week)	Total number of weeks	Total hours in term
Courses (Face-to-face teaching):	3	15
Own studies outside class:	6	15
Practice, Recitation:	0	0
Homework:	6	5
Term project:	0	0
Term project presentation:	0	0
Quiz:	0	0
Own study for mid-term exam:	0	0
Mid-term:	0	0
Personal studies for final exam:	3	6
Final exam:	3	1
		Total workload:
		Total ECTS credits:	*
	* ECTS credit is calculated by dividing total workload by 25. (1 ECTS = 25 work hours)