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| MBGL5030 | Advanced Bioinformatics | 3+0+0 | ECTS:7.5 | | Year / Semester | Fall Semester | | Level of Course | Second Cycle | | Status | Elective | | Department | DEPARTMENT of MOLECULAR BIOLOGY and GENETICS | | Prerequisites and co-requisites | None | | Mode of Delivery | | | Contact Hours | 14 weeks - 3 hours of lectures per week | | Lecturer | Doç. Dr. Halil İbrahim GÜLER | | Co-Lecturer | No | | Language of instruction | Turkish | | Professional practise ( internship ) | None | | | | The aim of the course: | | This course aims to enable students to apply fundamental bioinformatics tools and databases for protein and ligand modeling, docking, interaction analysis, virtual screening, ADMET evaluation, and molecular dynamics simulations in the context of drug discovery processes. |
| Programme Outcomes | CTPO | TOA | | Upon successful completion of the course, the students will be able to : | | | | PO - 1 : | Use protein and ligand modeling techniques to create target molecules in silico and prepare them in appropriate formats. | 3 | 1,2, | | PO - 2 : | Apply docking, interaction analysis, and virtual screening tools to evaluate protein?ligand binding models. | 8 | 1,2, | | PO - 3 : | Retrieve data from chemical, natural product, and pharmacophore databases, perform format conversions, and assess drug-likeness through ADMET analysis. | 8 | 1,2, | | PO - 4 : | Describe the basic stages of molecular dynamics simulations and apply them to a simple protein?ligand system. | 8 | 1,2, | | CTPO : Contribution to programme outcomes, TOA :Type of assessment (1: written exam, 2: Oral exam, 3: Homework assignment, 4: Laboratory exercise/exam, 5: Seminar / presentation, 6: Term paper), PO : Learning Outcome | | |
| The course covers protein modeling, the use of chemical and natural product databases, ligand preparation, docking applications, interaction and visualization analyses, virtual screening, and ADMET evaluations, concluding with an introduction to molecular dynamics simulations. |
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| Course Syllabus | | Week | Subject | Related Notes / Files | | Week 1 | Bioinformatics-related concepts; general introduction to the tools to be used. | | | Week 2 | Introduction to Basic Linux Commands. Terminal usage, file system structure, basic commands (ls, cd, pwd, mkdir, cp, mv, rm, etc.), file permissions, working with sample data files. | | | Week 3 | Protein Databases. UniProt, PDB; differences between protein sequence and structure; downloading from PDB; identifying target proteins. | | | Week 4 | 3D Protein Modeling (SWISS-MODEL, I-TASSER, RaptorX, AlphaFold). Homology modeling, ab initio, and AI-based modeling; template selection, model generation, quality assessment; comparison of the four platforms. | | | Week 5 | Chemical and Natural Product Databases. PubChem, ChEMBL, COCONUT, KNApSAcK, NPASS; keyword and structure-based search; data download and formatting; the role of natural products in drug discovery. | | | Week 6 | Molecule Drawing, Conversion, and Optimization. Ligand drawing, energy minimization, format conversion (MOL2, PDB, SDF); optimization of a sample ligand. | | | Week 7 | Molecular Docking Theory. Docking concepts, binding energies, scoring functions, AutoDock 4.2 workflow and file requirements. | | | Week 8 | | | | Week 9 | Molecular Docking with AutoDock 4.2. Protein and ligand preparation (AutoDockTools), grid box setup, running docking, interpreting results. | | | Week 10 | Protein?Ligand Interaction Analysis. 2D/3D interaction diagrams, preparation of publication-quality visuals, analysis of docking results. | | | Week 11 | Advanced 3D Visualization and Structure Manipulation. High-quality 3D rendering, multi-structure display, structure editing, special analyses (electrostatic potential, distance/angle measurement). | | | Week 12 | ADMET Analysis. Concepts of ADME and toxicity, SwissADME, pkCSM, Lipinski?s rules; ADMET compliance analysis. | | | Week 13 | Virtual Screening. Using Pharmit, pharmacophore-based screening, selection of ADMET-compliant compounds. | | | Week 14 | Reverse Docking with PharmMapper. Ligand-based target prediction, PharmMapper principles and applications. | | | Week 15 | Introduction to Molecular Dynamics (MD) Simulations. Purpose and applications of MD; energy minimization, equilibration (NVT, NPT), production stage; force fields; overview of GROMACS. | | | Week 16 | Final Exam | | | |
| 1 | Öğretim elemanının notları | | | |
| Method of Assessment | | Type of assessment | Week No | Date | Duration (hours) | Weight (%) | | Mid-term exam | 9 | | 2 | 35 | | Homework/Assignment/Term-paper | 15 | | 1 | 15 | | End-of-term exam | 16 | | 2 | 50 | | |
| Student Work Load and its Distribution | | Type of work | Duration (hours pw) | No of weeks / Number of activity | Hours in total per term | | Yüz yüze eğitim | 3 | 14 | 42 | | Sınıf dışı çalışma | 6 | 16 | 96 | | Arasınav için hazırlık | 4 | 8 | 32 | | Arasınav | 1 | 1 | 1 | | Ödev | 1 | 2 | 2 | | Dönem sonu sınavı için hazırlık | 3 | 16 | 48 | | Dönem sonu sınavı | 1 | 1 | 1 | | Total work load | | | 222 |
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