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

Learning outcomes

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

1. Visualize three dimensional structures of proteins using scientific software

   Contribution to Program Outcomes

   1. Acquire knowledge on biological, chemical, physical and mathematical principles which constitute the basis of bioengineering applications
   2. Acquire knowledge on current bioengineering applications from the industrial and scientific aspects
   3. Acquire knowledge for research methods which are required to develop novel application methods
   4. Design processes for the investigation of bioengineering problems, collect data, analyze and interpret the results.
   5. Combine, Interpret, and analyze different subfields of bioengineering

   Method of assessment

   1. Homework assignment
   2. Laboratory exercise/exam
2. Conduct basic analyses of biomolecular simulation trajectories

   Contribution to Program Outcomes

   1. Acquire knowledge on current bioengineering applications from the industrial and scientific aspects
   2. Acquire knowledge for research methods which are required to develop novel application methods
   3. Apply mathematical analysis and modeling methods for bioengineering design and production processes.

   Method of assessment

   1. Homework assignment
   2. Laboratory exercise/exam
3. Generate structural models of protein-small molecule interactions

   Contribution to Program Outcomes

   1. Convert biological, chemical, physical and mathematical principles into novel applications for the benefit of society,
   2. Apply mathematical analysis and modeling methods for bioengineering design and production processes.
   3. Conduct and develop bioengineering applications for relevant sectors such as health and agricultural industry.
   4. Design processes for the investigation of bioengineering problems, collect data, analyze and interpret the results.

   Method of assessment

   1. Homework assignment
   2. Laboratory exercise/exam
4. Identify drug candidate small molecules using virtual screening

   Contribution to Program Outcomes

   1. Acquire knowledge on current bioengineering applications from the industrial and scientific aspects
   2. Acquire knowledge for research methods which are required to develop novel application methods
   3. Convert biological, chemical, physical and mathematical principles into novel applications for the benefit of society,
   4. Apply mathematical analysis and modeling methods for bioengineering design and production processes.
   5. Combine, Interpret, and analyze different subfields of bioengineering
   6. Work effectively in multi-disciplinary research teams

   Method of assessment

   1. Homework assignment
   2. Laboratory exercise/exam
5. Define the basic concepts used in structure and ligand-based drug discovery with computational methods.

   Contribution to Program Outcomes

   1. Acquire knowledge on biological, chemical, physical and mathematical principles which constitute the basis of bioengineering applications
   2. Acquire knowledge on current bioengineering applications from the industrial and scientific aspects
   3. Acquire knowledge for research methods which are required to develop novel application methods

   Method of assessment

   1. Written exam

Contents
Week 1:	Introduction to drug discovery and development
Week 2:	Basic principles of computer-aided drug discovery
Week 3:	Introduction to chem- and bio-informatics databases
Week 4:	Querying ChEMBL and Protein Data Bank programmatically
Week 5:	Molecular filtering based on pairwise compound similarity measures Homework I
Week 6:	Maximum common substructure method
Week 7:	Ligand-based screening: machine-learning Homework II
Week 8:	Ligand-based pharmacophore models Mid-term Exam
Week 9:	Prediction of interactions between drug candidates and protein structures: molecular docking simulations Homework III
Week 10:	Visualization and analysis of protein-ligand interactions
Week 11:	Docking-based virtual screening
Week 12:	Protein-ligand molecular dynamics simulation (preparation, production)
Week 13:	Analysis of protein-ligand MD simulation results
Week 14:	Term project presentations
Week 15*:	-
Week 16*:	Final Exam
Textbooks and materials:	Textbooks: G. Petsko, Ringe, D., Protein Structure and Function, 2003, Wiley-Blackwell A. Leach, Molecular Modeling: Principles and Applications, 2nd Ed., 2002, Pearson N. Ben-Tal, Kessel, A., Introduction to Proteins: Structure, Function, and Motion, Second Edition, 2018, CRC Press K. Merz, D. Ringe, C.H. Reynolds (ed.), Drug Design: Structure- and Ligand-Based Approaches, 2010, Cambridge University Press Other tutorials and papers
Recommended readings:	A. Liljas, L. Liljas, J. Piskur, Textbook of Structural Biology, 2009, WSPC I. Bahar, R. L. Jernigan, Protein Actions: Principles and Modeling, 2017, Garland Science
	* 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:	8	20
Other in-term studies:		0
Project:	14	20
Homework:	5, 7, 9	20
Quiz:		0
Final exam:	16	40
	Total weight:	(%)

Workload
Activity	Duration (Hours per week)	Total number of weeks	Total hours in term
Courses (Face-to-face teaching):	3	13
Own studies outside class:	2	14
Practice, Recitation:	0	0
Homework:	2	3
Term project:	3	5
Term project presentation:	1	3
Quiz:	0	0
Own study for mid-term exam:	3	5
Mid-term:	2	1
Personal studies for final exam:	3	5
Final exam:	2	1
		Total workload:
		Total ECTS credits:	*
	* ECTS credit is calculated by dividing total workload by 25. (1 ECTS = 25 work hours)