| MATHEMATICS (TURKISH, PHD) | |||||
| PhD | TR-NQF-HE: Level 8 | QF-EHEA: Third Cycle | EQF-LLL: Level 8 | ||
| Course Code | Course Name | Semester | Theoretical | Practical | Credit | ECTS |
| MED2017 | Introduction to Molecular Modeling and Simulations | Fall | 2 | 2 | 2 | 2 |
| The course opens with the approval of the Department at the beginning of each semester |
| Language of instruction: | En |
| Type of course: | Departmental Elective |
| Course Level: | |
| Mode of Delivery: | Face to face |
| Course Coordinator : | Prof. Dr. SERDAR DURDAĞI |
| Course Lecturer(s): |
Prof. Dr. SERDAR DURDAĞI |
| Course Objectives: | Introduction to Molecular Modeling and Simulations provides an introduction into modeling and simulation approaches, covering continuum methods, atomistic simulation (e.g. molecular docking, molecular dynamics) as well as quantum mechanics. Atomistic and molecular simulation methods are new tools that allow one to predict structural and dynamical properties of small molecules and macromolecules (i.e., proteins). This approach is an exciting new paradigm that allows to design novel materials and structures from the bottom up — to make materials with improved properties. |
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The students who have succeeded in this course; 1. Understand the basic principles and concepts of protein structure, 3D-QSAR, molecular docking, molecular dynamics simulations, and computer-aided drug discovery 2. Set up and run their own protein / biomolecular system MD simulations on personal computers 3. Perform and understand the interpretation of basic (statistical) analysis techniques on the resulting MD trajectories 4. Perform and understand the results of a virtual screening experiment |
| 1. Introduction to protein structure and visualization 2. Introduction to ligand-based and structure-based drug design techniques 3. Introduction to 3D-QSAR (theory) 4. Introduction to 3D-QSAR (application) 5. Introduction to Molecular Docking Simulations (theory) 6. Introduction to Molecular Docking Simulations (application) 7. Introduction to MD simulations-part1 8. Introduction to MD simulations-part2 9. Introduction to MD simulations (application) 10. Introduction to MD simulations (application) 11. Post-processing MD simulations (theory) 12. Post-processing MD simulations (application) 13. Student project-1 14. Student project-2 |
| Week | Subject | Related Preparation |
| Course Notes: | Molecular Modelling: Principles and Applications, by Andrew Leach http://www.amazon.com/Molecular-Modelling-Applications-Andrew-Leach/dp/0582239338 Molecular Modeling and Simulation, by Tamar Schlick http://www.amazon.com/Molecular-Modeling-Simulation-Tamar-Schlick/dp/038795404X |
| References: | Introduction to Protein Structure: Second Edition, by Carl Branden and John Tooze http://www.amazon.com/Introduction-Protein-Structure-Carl-Branden/dp/0815323050 |
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