Syllabus ( BSB 533 )
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Basic information
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Course title: |
Computational Biomolecular Dynamics |
Course code: |
BSB 533 |
Lecturer: |
Assist. Prof. Onur SERÇİNOĞLU
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ECTS credits: |
7.5 |
GTU credits: |
3 (3+0+0) |
Year, Semester: |
1/2, Spring |
Level of course: |
Second Cycle (Master's) |
Type of course: |
Area Elective
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Language of instruction: |
English
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Mode of delivery: |
Face to face
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Pre- and co-requisites: |
BSB511 |
Professional practice: |
No |
Purpose of the course: |
The aim of this course is to provide students with the basic knowledge and skills necessary to use the methods used in the simulation of the structural dynamical behavior of biological macromolecules, with a particular focus on protein structures. |
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Learning outcomes
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Upon successful completion of this course, students will be able to:
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Choose appropriate biomolecular dynamics simulation methods in accordance with the intended purpose.
Contribution to Program Outcomes
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Define and manipulate basic and advanced concepts in the field of Bioinformatics and Systems Biology
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Formulate, code, solve and analyze problems on biomolecular interactions by using an engineering viewpoint.
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Acquire scientific knowledge and work independently
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Develop an awareness of continuous learning in relation with modern technology
Method of assessment
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Written exam
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Homework assignment
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Apply software used to simulate dynamic behaviour of biological macromolecules.
Contribution to Program Outcomes
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Define and manipulate basic and advanced concepts in the field of Bioinformatics and Systems Biology
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Formulate, code, solve and analyze problems on biomolecular interactions by using an engineering viewpoint.
Method of assessment
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Homework assignment
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List methods used to simulate biological macromolecular dynamics.
Contribution to Program Outcomes
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Define and manipulate basic and advanced concepts in the field of Bioinformatics and Systems Biology
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Formulate, code, solve and analyze problems on biomolecular interactions by using an engineering viewpoint.
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Effectively express his/her research ideas and findings both orally and in writing
Method of assessment
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Written exam
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Contents
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Week 1: |
Protein structure, folding, function, and dynamics |
Week 2: |
Introduction to methods for simulation of biomolecular dynamics |
Week 3: |
Equations of motion and molecular mechanics force-fields Homework I |
Week 4: |
Classical molecular dynamics simulations of biomolecular dynamics |
Week 5: |
Monte-Carlo simulations of biomolecular dynamics Homework II |
Week 6: |
Essential dynamics analysis of biomolecular simulation trajectories |
Week 7: |
Network analysis of biomolecular simulation trajectories Homework III |
Week 8: |
Enhanced sampling methods |
Week 9: |
Steered molecular dynamics Homework IV |
Week 10: |
Free energy methods: umbrella sampling Term project |
Week 11: |
Simulations of transmembrane protein dynamics Term project |
Week 12: |
Elastic network models Term project |
Week 13: |
Simulation case studies Term project |
Week 14: |
Case studies on molecular dynamics simulations in drug discovery Term project presentations |
Week 15*: |
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Week 16*: |
Final exam |
Textbooks and materials: |
Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes: From Bioinformatics to Molecular Quantum Mechanics, 2014, Ed: Adam Liwo
Protein Actions: Principles and Modeling, 2017, Iver Bahar, Robert Jernigan, Ken A Dill
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Recommended readings: |
Molecular Modelling: Principles and Applications, 2002, Andrew Leach |
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* Between 15th and 16th weeks is there a free week for students to prepare for final exam.
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Assessment
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Method of assessment |
Week number |
Weight (%) |
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Mid-terms: |
3 |
0 |
Other in-term studies: |
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0 |
Project: |
10, 11, 12, 13, 14 |
40 |
Homework: |
3, 5, 7, 9 |
20 |
Quiz: |
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0 |
Final exam: |
16 |
40 |
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Total weight: |
(%) |
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Workload
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Activity |
Duration (Hours per week) |
Total number of weeks |
Total hours in term |
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Courses (Face-to-face teaching): |
3 |
14 |
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Own studies outside class: |
3 |
14 |
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Practice, Recitation: |
2 |
6 |
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Homework: |
6 |
4 |
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Term project: |
8 |
4 |
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Term project presentation: |
1 |
1 |
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Quiz: |
0 |
0 |
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Own study for mid-term exam: |
0 |
0 |
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Mid-term: |
0 |
0 |
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Personal studies for final exam: |
4 |
8 |
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Final exam: |
3 |
1 |
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Total workload: |
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Total ECTS credits: |
* |
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* ECTS credit is calculated by dividing total workload by 25. (1 ECTS = 25 work hours)
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