BIO604 Advanced Structural Bioinformatics
BIO604 Advanced Structural Bioinformatics
Syllabus | International University of Sarajevo - Last Update on Oct 10, 2025
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Genetics and Bioengineering
Betul Akcesme
Course Lecturer
Course Objectives
This course aims to expand the knowledge of students about the prediction and analysis of the three-dimensional structures of biological macromolecules (protein, RNA and DNA) and to explain the structure & function relationship and their importance in advanced level.
Learning Outcomes
After successful completion of the course, the student will be able to:
Course Materials
Required Textbook
Introduction to Protein Structure,Branden, Carl, and John Tooze.. 2nd ed. New York, NY: Garland Science, 1999. ISBN: 9780815323051. Textbook Of Structural Biology , by Liljas , Piskur ,Lindblom, Nissen, Kjeldgaard , World scientific publishing, ISBN-13: 978-9812772084. Protein structure and Function, G. Petsko and D. Ringe, Oxford University Press, 2009,
Additional Literature
Structural Bioinformatics,Gu and Bourne, Wiley second editionTeaching Methods
Lecturing by using PPT presentations. Article discussion
Book chapters
Project design
Weekly Topics
| Week | Topic | Readings / References |
|---|---|---|
| 1 | Introduction to Structural Bioinformatics | TBA |
| 2 | Fundamentals of Protein structure | TBA |
| 3 | Data presentation and Databases(RCSB-PDB, PDBe-KB, Uniprot, GWAS) | TBA |
| 4 | Structural bioinformatics applications and project design | TBA |
| 5 | Homology modelling, Threading ve denovo modelling | TBA |
| 6 | Structural Quality Assurance (procheck- whatcheck) | TBA |
| 7 | Bioinformatics tools for protein structure analysis II (article discussion) | TBA |
| 8 | MIDTERM | TBA |
| 9 | Structure-based drug discovery/ Molecular Docking | TBA |
| 10 | Effects of mutations of protein structure and function | TBA |
| 11 | Project progression and discussion | TBA |
| 12 | Protein structure determinations- (article discussion) | TBA |
| 13 | Protein structure analysis and classification: InterPro, Pfam, CATH | TBA |
| 14 | Further applications of structural bioinformatics in medicine | TBA |
| 15 | Project evaluation and presentation |
Course Schedule (All Sections)
| Section | Type | Day 1 | Venue 1 | Day 2 | Venue 2 |
|---|---|---|---|---|---|
| BIO604.1 | Course | Wednesday 17:00 - 19:50 | A F1.25 | - | - |
Office Hours & Room
| Day | Time | Office | Notes |
|---|---|---|---|
| Monday | 11:00 - 13:00 | A F1.34 | |
| Wednesday | 12:00 - 14:00 | A F1.34 |
Assessment Methods and Criteria
Assessment Components
Final Exam
AI: Not AllowedAlignment with Learning Outcomes : 1 2 3 4 5
Midterm exam
AI: Not AllowedAlignment with Learning Outcomes : 1 2 3 4 5
Homeworks
AI: Not AllowedAlignment with Learning Outcomes : 1 2 3 4 5
Term project presentation
AI: Not AllowedAlignment with Learning Outcomes : 1 2 3 4 5
IUS Grading System
| Grading Scale | IUS Grading System | IUS Coeff. | Letter (B&H) | Numerical (B&H) |
|---|---|---|---|---|
| 0 - 44 | F | 0 | F | 5 |
| 45 - 54 | E | 1 | ||
| 55 - 64 | C | 2 | E | 6 |
| 65 - 69 | C+ | 2.3 | D | 7 |
| 70 -74 | B- | 2.7 | ||
| 75 - 79 | B | 3 | C | 8 |
| 80 - 84 | B+ | 3.3 | ||
| 85 - 94 | A- | 3.7 | B | 9 |
| 95 - 100 | A | 4 | A | 10 |
Late Work Policy
Information about late submission policies will be shared during class and posted in this section. Please check back for official guidelines.
ECTS Credit Calculation
📚 Student Workload
This 6 ECTS credit course corresponds to 150 hours of total student workload, distributed as follows:
Lecture hours
45 hours ⏳ (15 week × 3 h)
Project presentation
18 hours ⏳ (3 week × 6 h)
Home study
15 hours ⏳ (15 week × 1 h)
Midterm exam study
26 hours ⏳ (2 week × 13 h)
Final exam study
30 hours ⏳ (3 week × 10 h)
Homework
16 hours ⏳ (4 week × 4 h)
150 Total Workload Hours
6 ECTS Credits
Course Policies
Academic Integrity
All work submitted must be your own. Plagiarism, cheating, or any form of academic dishonesty will result in disciplinary action according to university policies. When in doubt about citation practices, consult the instructor.
Attendance Policy
Students are expected to adhere to the attendance requirements as outlined in the International University of Sarajevo Study Rules and Regulations. Excessive absences, whether excused or unexcused, may impact academic performance and eligibility for assessment. Mandatory sessions (e.g., labs, workshops) require attendance unless formally exempted. For detailed policies on absences, documentation, and penalties, please refer to the official university regulations.
Technology & AI Policy
Laptops/tablets may be used for note-taking only during lectures. Phones should be silenced and put away during all class sessions. Audio/video recording requires prior permission from the instructor.
Artificial Intelligence (AI) Usage: The use of AI tools (e.g., ChatGPT, Copilot, Gemini) varies by assessment component. Please refer to the AI usage indicator next to each assessment item in the Assessment Methods and Criteria section above. Submitting AI-generated content as your own work, where AI is not explicitly allowed, constitutes an academic integrity violation.
Communication Policy
All course-related communication should occur through official university channels (institutional email or SIS). Emails should include [BIO604] in the subject line.
Academic Quality Assurance Policy
Course Academic Quality Assurance is achieved through Semester Student Survey. At the end of each academic year, the institution of higher education is obliged to evaluate work of the academic staff, or the success of realization of the curricula.
Learning Tips
Be prepared to contribute thoughtfully during class discussions, labs, or collaborative work. Active participation deepens understanding and encourages critical thinking.
Complete assigned readings or prep materials before class. Take notes, highlight key ideas, and jot down questions. Aim to grasp core concepts and their applications—not just facts.
Use course frameworks or methodologies to analyze problems, case studies, or projects. Begin early to allow time for reflection and refinement. Seek feedback to improve your work.
Don’t hesitate to reach out when something is unclear. Use office hours, discussion boards, or peer networks to clarify concepts and stay on track.
Syllabus Last Updated on Oct 10, 2025 | International University of Sarajevo
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Referencing Curricula Print this page
| Course Code | Course Title | Weekly Hours* | ECTS | Weekly Class Schedule | ||||||
| T | P | |||||||||
| BIO604 | Advanced Structural Bioinformatics | 0 | 3 | 6 | ||||||
| Prerequisite | None | It is a prerequisite to | - | |||||||
| Lecturer | Betul Akcesme | Office Hours / Room / Phone | Monday: 11:00-13:00 Wednesday: 12:00-14:00 |
|||||||
| bakcesme@ius.edu.ba | ||||||||||
| Assistant | Assistant E-mail | |||||||||
| Course Objectives | This course aims to expand the knowledge of students about the prediction and analysis of the three-dimensional structures of biological macromolecules (protein, RNA and DNA) and to explain the structure & function relationship and their importance in advanced level. | |||||||||
| Textbook | Introduction to Protein Structure,Branden, Carl, and John Tooze.. 2nd ed. New York, NY: Garland Science, 1999. ISBN: 9780815323051. Textbook Of Structural Biology , by Liljas , Piskur ,Lindblom, Nissen, Kjeldgaard , World scientific publishing, ISBN-13: 978-9812772084. Protein structure and Function, G. Petsko and D. Ringe, Oxford University Press, 2009, | |||||||||
| Additional Literature |
|
|||||||||
| Learning Outcomes | After successful completion of the course, the student will be able to: | |||||||||
|
||||||||||
| Teaching Methods | Lecturing by using PPT presentations. Article discussion, Book chapters, project design | |||||||||
| Teaching Method Delivery | Face-to-face | Teaching Method Delivery Notes | ||||||||
| WEEK | TOPIC | REFERENCE | ||||||||
| Week 1 | Introduction to Structural Bioinformatics | TBA | ||||||||
| Week 2 | Fundamentals of Protein structure | TBA | ||||||||
| Week 3 | Data presentation and Databases(RCSB-PDB, PDBe-KB, Uniprot, GWAS) | TBA | ||||||||
| Week 4 | Structural bioinformatics applications and project design | TBA | ||||||||
| Week 5 | Homology modelling, Threading ve denovo modelling | TBA | ||||||||
| Week 6 | Structural Quality Assurance (procheck- whatcheck) | TBA | ||||||||
| Week 7 | Bioinformatics tools for protein structure analysis II (article discussion) | TBA | ||||||||
| Week 8 | MIDTERM | TBA | ||||||||
| Week 9 | Structure-based drug discovery/ Molecular Docking | TBA | ||||||||
| Week 10 | Effects of mutations of protein structure and function | TBA | ||||||||
| Week 11 | Project progression and discussion | TBA | ||||||||
| Week 12 | Protein structure determinations- (article discussion) | TBA | ||||||||
| Week 13 | Protein structure analysis and classification: InterPro, Pfam, CATH | TBA | ||||||||
| Week 14 | Further applications of structural bioinformatics in medicine | TBA | ||||||||
| Week 15 | Project evaluation and presentation | |||||||||
| Assessment Methods and Criteria | Evaluation Tool | Quantity | Weight | Alignment with LOs | AI Usage |
| Final Exam | 1 | 40 | 1,2,3,4,5 | Not Allowed | |
| Semester Evaluation Components | |||||
| Midterm exam | 1 | 30 | 1, 2, 3, 4, 5 | Not Allowed | |
| Homeworks | 2 | 20 | 1, 2, 3, 4, 5 | Not Allowed | |
| Term project presentation | 1 | 10 | 1, 2, 3, 4, 5 | Not Allowed | |
| *** ECTS Credit Calculation *** | |||||
| Activity | Hours | Weeks | Student Workload Hours | Activity | Hours | Weeks | Student Workload Hours | |||
| Lecture hours | 3 | 15 | 45 | Project presentation | 6 | 3 | 18 | |||
| Home study | 1 | 15 | 15 | Midterm exam study | 13 | 2 | 26 | |||
| Final exam study | 10 | 3 | 30 | Homework | 4 | 4 | 16 | |||
| Total Workload Hours = | 150 | |||||||||
| *T= Teaching, P= Practice | ECTS Credit = | 6 | ||||||||
| Course Academic Quality Assurance: Semester Student Survey | Last Update Date: 23/10/2025 | |||||||||