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Description of Individual Course Units

Course Unit Code Course Unit Title Type Of Course D U L ECTS BST 5002 INTRODUCTION TO MOLECULAR MODELLING ELECTIVE 3 0 0 9

Offered By

Biomedicine and Health Technologies

Level of Course Unit

Second Cycle Programmes (Master's Degree)

Course Coordinator

ASSISTANT PROFESSOR EZGI KARACA EREK

Offered to

Biomedicine and Health Technologies

Course Objective

Learning Outcomes of the Course Unit

1   Learning basics of structural biology 2   Learning basics of mathematical modeling 3   Learning how web-servers can be applied to model proteins and nucleic acids 4   Learning how to design an in silico experiment 5   Learning how to interpret in silico experiment results

Mode of Delivery

Face -to- Face

Prerequisites and Co-requisites

None

Recomended Optional Programme Components

None

Course Contents

Week Subject Description 1 Introduction to Protein structures 2 Introduction to Protein folding and flexibility 3 Introduction to DNA structure and its recognition by proteins 4 Introduction to RNA structure and its recognition by proteins 5 Introduction to Protein Families 6 Experimental Structure Determination Methods 7 Computational Structure Determination Techniques 8 Empirical Force Fields 9 Potential energy surfaces, energy minimization methods 10 Classical mechanics and molecular dynamics 11 Basic statistical mechanics and monte carlo 12 The use of evolutionary conservation in molecular modeling 13 Homology Modeling by web-servers 14 Biomolecular Docking by web-servers 15 Protein design by web-servers 16 FINAL EXAM

Recomended or Required Reading

To be announced.

Planned Learning Activities and Teaching Methods

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

To be announced.

Language of Instruction

English

Course Policies and Rules

To be announced.

Contact Details for the Lecturer(s)

To be announced.

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 5 70 Preparation for midterm exam 1 15 15 Preparation for final exam 1 20 20 Preparing assignments 1 50 50 Preparing presentations 1 15 15 Final 1 10 10 Midterm 1 5 5 TOTAL WORKLOAD (hours) 230

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 5 5 LO.2 5 5 5 5 LO.3 5 5 5 5 LO.4 5 5 5 5 5 5 5 LO.5 5 5 5 5 5 5 5