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Syllabus ( BSB 533 )


   Basic information
Course title: Computational Biomolecular Dynamics
Course code: BSB 533
Lecturer: Assist. Prof. Onur SERÇİNOĞLU
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
Language of instruction: English
Mode of delivery: Face to face
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.
   Learning outcomes Up

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

  1. Choose appropriate biomolecular dynamics simulation methods in accordance with the intended purpose.

    Contribution to Program Outcomes

    1. Define and manipulate basic and advanced concepts in the field of Bioinformatics and Systems Biology
    2. Formulate, code, solve and analyze problems on biomolecular interactions by using an engineering viewpoint.
    3. Acquire scientific knowledge and work independently
    4. Develop an awareness of continuous learning in relation with modern technology

    Method of assessment

    1. Written exam
    2. Homework assignment
  2. Apply software used to simulate dynamic behaviour of biological macromolecules.

    Contribution to Program Outcomes

    1. Define and manipulate basic and advanced concepts in the field of Bioinformatics and Systems Biology
    2. Formulate, code, solve and analyze problems on biomolecular interactions by using an engineering viewpoint.

    Method of assessment

    1. Homework assignment
  3. List methods used to simulate biological macromolecular dynamics.

    Contribution to Program Outcomes

    1. Define and manipulate basic and advanced concepts in the field of Bioinformatics and Systems Biology
    2. Formulate, code, solve and analyze problems on biomolecular interactions by using an engineering viewpoint.
    3. Effectively express his/her research ideas and findings both orally and in writing

    Method of assessment

    1. Written exam
   Contents Up
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*: -
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


Recommended readings: Molecular Modelling: Principles and Applications, 2002, Andrew Leach
  * Between 15th and 16th weeks is there a free week for students to prepare for final exam.
Assessment Up
Method of assessment Week number Weight (%)
Mid-terms: 3 0
Other in-term studies: 0
Project: 10, 11, 12, 13, 14 40
Homework: 3, 5, 7, 9 20
Quiz: 0
Final exam: 16 40
  Total weight:
(%)
   Workload Up
Activity Duration (Hours per week) Total number of weeks Total hours in term
Courses (Face-to-face teaching): 3 14
Own studies outside class: 3 14
Practice, Recitation: 2 6
Homework: 6 4
Term project: 8 4
Term project presentation: 1 1
Quiz: 0 0
Own study for mid-term exam: 0 0
Mid-term: 0 0
Personal studies for final exam: 4 8
Final exam: 3 1
    Total workload:
    Total ECTS credits:
*
  * ECTS credit is calculated by dividing total workload by 25.
(1 ECTS = 25 work hours)
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