MEDICINE
Bachelor TR-NQF-HE: Level 6 QF-EHEA: First Cycle EQF-LLL: Level 6

Course Introduction and Application Information

Course Code Course Name Semester Theoretical Practical Credit ECTS
MED2017 Introduction to Molecular Modeling and Simulations Spring 2 2 2 2
This catalog is for information purposes. Course status is determined by the relevant department at the beginning of semester.

Basic information

Language of instruction: English
Type of course: Departmental Elective
Course Level: Bachelor’s Degree (First Cycle)
Mode of Delivery: Face to face
Course Coordinator : Prof. Dr. SERDAR DURDAĞI
Course Lecturer(s): Prof. Dr. SERDAR DURDAĞI
Recommended Optional Program Components: None
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.

Learning Outcomes

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

Course Content

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

Weekly Detailed Course Contents

Week Subject Related Preparation

Sources

Course Notes / Textbooks: 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

Evaluation System

Semester Requirements Number of Activities Level of Contribution
Total %
PERCENTAGE OF SEMESTER WORK % 0
PERCENTAGE OF FINAL WORK %
Total %

Contribution of Learning Outcomes to Programme Outcomes

No Effect 1 Lowest 2 Low 3 Average 4 High 5 Highest
           
Program Outcomes Level of Contribution
1) Integrates the knowledge, skills and attitudes acquired from basic and clinical medical sciences, behavioral sciences and social sciences, and uses them in health service delivery.
2) In patient management, shows a biopsychosocial approach that takes into account the socio-demographic and sociocultural background of the individual, regardless of language, religion, race and gender.
3) In the provision of health services, prioritizes the protection and development of the health of individuals and society.
4) Taking into account the individual, societal, social and environmental factors affecting health; does the necessary work to maintain and improve the state of health.
5) By recognizing the characteristics, needs and expectations of the target audience, provides health education to healthy/sick individuals and their relatives and other healthcare professionals.
6) Shows a safe, rational and effective approach in health service delivery, prevention, diagnosis, treatment, follow-up and rehabilitation processes.
7) Performs invasive and/or non-invasive procedures in diagnosis, treatment, follow-up and rehabilitation processes in a safe and effective way for the patient.
8) Provides health services by considering patient and employee health and safety.
9) In the provision of health services, takes into account the changes in the physical and socioeconomic environment on a regional and global scale, as well as the changes in the individual characteristics and behaviors of the people who apply to it.
10) Takes good medical practice into account while carrying out his/her profession.
11) Fulfills its duties and obligations within the framework of ethical principles, rights and legal responsibilities required by its profession.
12) Demonstrates decisive behavior in providing high-quality health care, taking into account the integrity of the patient.
13) Evaluates his/her performance in his/her professional practice by considering his/her emotions and cognitive characteristics.
14) Advocates improving the provision of health services by considering the concepts of social reliability and social responsibility for the protection and development of public health.
15) Can plan and carry out service delivery, training and consultancy processes related to individual and community health in cooperation with all components for the protection and development of health.
16) Evaluates the impact of health policies and practices on individual and community health indicators and advocates increasing the quality of health services.
17) The physician attaches importance to the protection of his/her own physical, mental and social health, and does what is necessary for this
18) Shows exemplary behavior and leads the healthcare team during service delivery.
19) Uses resources cost-effectively, for the benefit of society and in accordance with the legislation, in the planning, implementation and evaluation processes of health services in the health institution he/she is the manager of.
20) Establishes positive communication within the health team it serves and assumes different team roles when necessary.
21) Is aware of the duties and responsibilities of the health workers in the health team and acts accordingly.
22) In the professional practices, works in harmony and effectively with the colleagues and other professional groups.
23) Communicates effectively with patients, their relatives, healthcare professionals, other professional groups, institutions and organizations.
24) Communicates effectively with individuals and groups that require a special approach and have different socio-cultural characteristics.
25) In the diagnosis, treatment, follow-up and rehabilitation processes, shows a patient-centered approach that associates the patient with the decision-making mechanisms.
26) Plans and implements scientific research, when necessary, for the population it serves, and uses the results and/or the results of other research for the benefit of the society.
27) Reaches and critically evaluates current literature knowledge about his/her profession.
28) Applies the principles of evidence-based medicine in clinical decision making.
29) Uses information technologies to increase the effectiveness of its work on health care, research and education.
30) Effectively manages individual work processes and career development.
31) Demonstrates skills in acquiring and evaluating new knowledge, integrating it with existing knowledge, applying it to professional situations and adapting to changing conditions throughout professional life.
32) Selects the right learning resources to improve the quality of the health service it offers, organizes its own learning process