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Description of Individual Course Units

Course Unit Code Course Unit Title Type Of Course D U L ECTS MBG 6134 ADVANCED COMPUTATIONAL STRUCTURAL BIOLOGY TECHNIQUES ELECTIVE 3 0 0 12

Offered By

Molecular Biology and Genetics

Level of Course Unit

Third Cycle Programmes (Doctorate Degree)

Course Coordinator

ASSISTANT PROFESSOR EZGI KARACA EREK

Offered to

Molecular Biology and Genetics Molecular Biology and Genetics

Course Objective

To have a comprehensive understanding of how biomolecules can be modeled through diverse computational techniques.

Learning Outcomes of the Course Unit

1   1. Learning advanced structural biology 2   2. Learning advanced mathematical modeling 3   3. Learning how algorithms can be applied to model proteins and nucleic acids 4   4. Learning how to design a complex in silico experiment 5   5. Learning how to interpret in silico experiment results and devise new experiments from them

Mode of Delivery

Face -to- Face

Prerequisites and Co-requisites

None

Recomended Optional Programme Components

None

Course Contents

Week Subject Description 1 Protein structure and its post-translational modifications 2 Protein folding phenomena 3 DNA structure and its post-translational modifications 4 RNA structure and its post-translational modifications 5 Determination of Biomolecular Families through Evolution 6 Advanced Experimental Structure Determination Methods 7 Advanced Computational Structure Determination Techniques 8 Assessment of the Empirical Force Fields 9 Coding of Potential energy surfaces, energy minimization methods 10 Applied Classical mechanics and molecular dynamics 11 Advanced statistical mechanics and monte carlo 12 Integrating evolutionary conservation methods into molecular modeling 13 Homology Modeling by coding 14 Biomolecular Docking by coding 15 Protein Design by coding 16 Final exam

Recomended or Required Reading

A.E. Leach, Molecular Modelling: Principles and Applications, 2nd edition C. Brandon & J. Tooze, Introduction to Protein Structure, 2nd edition

Planned Learning Activities and Teaching Methods

Theoretical PowerPoint lectures with literature review/discussion, applied computer practicals.

Assessment Methods

SORTING NUMBER SHORT CODE LONG CODE FORMULA 1 ASG ASSIGNMENT 2 MTE MIDTERM EXAM 3 FIN FINAL EXAM 4 FCG FINAL COURSE GRADE ASG * 0.30 + MTE * 0.30 + FIN * 0.40 5 RST RESIT 6 FCGR FINAL COURSE GRADE (RESIT) ASG * 0.30 + MTE * 0.30 + RST * 0.40

Further Notes About Assessment Methods

None

Assessment Criteria

One minute paper should be delivered by the end of each lecture to the instructor. This paper should contain a couple of sentences summarizing what was taught during the lecture.

Language of Instruction

English

Course Policies and Rules

To be announced.

Contact Details for the Lecturer(s)

ezgi.karaca@deu.edu.tr

Office Hours

To be announced.

Work Placement(s)

None

Workload Calculation

Activities Number Time (hours) Total Work Load (hours) Lectures 15 3 45 Preparations before/after weekly lectures 14 8 112 Preparation for final exam 1 30 30 Preparing assignments 2 20 40 Project Preparation 1 45 45 Preparing presentations 2 15 30 Final 1 5 5 TOTAL WORKLOAD (hours) 307

Contribution of Learning Outcomes to Programme Outcomes

PO/LO PO.1 PO.2 PO.3 PO.4 PO.5 PO.6 PO.7 PO.8 LO.1 5 4 LO.2 5 4 LO.3 4 4 LO.4 4 4 4 4 LO.5 4 4 4