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| TBB6025 | Protein and Pathway Analysis | 2+2+0 | ECTS:7.5 | | Year / Semester | Spring Semester | | Level of Course | Third Cycle | | Status | Elective | | Department | DEPARTMENT of BIOSTATISTICS and MEDICAL INFORMATICS | | Prerequisites and co-requisites | None | | Mode of Delivery | Face to face, Practical | | Contact Hours | 14 weeks - 2 hours of lectures and 2 hours of practicals per week | | Lecturer | -- | | Co-Lecturer | Assist. Prof. Dr. Cihan İNAN, Assist. Prof. Dr. Uğur UZUNER | | Language of instruction | Turkish | | Professional practise ( internship ) | None | | | | The aim of the course: | | Upon completion the course, students will:
Be able to utilize the Protein Bioinformatics Databases and Resources towards drug discovery
Enable to employ the UniProt protein knowledgebase for diverse bioinformatics analyses
Utilize various bioinformatics tools to perform protein 3D structure prediction and deep analysis.
Understand how to reach and use the cell-signaling pathways for both biological and computational perspective.
Be able to develop knowledge-based models and bioinformatics workflows to identify protein players responsible for development of various human diseases. |
| Programme Outcomes | CTPO | TOA | | Upon successful completion of the course, the students will be able to : | | | | PO - 1 : | Understand the structure-function relationships of proteins | | 1,3 | | PO - 2 : | Model and analyse a given protein sequence to the structure | | 1,3 | | PO - 3 : | Perform 3D structural analysis of proteins and disease related receptors | | 1,3 | | PO - 4 : | Bioinformatically identify key regulator proteins and the'ir roles for a variety of different diseases | | 1,3 | | 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 | | |
| Introduction to biological macromolecules and structures; Protein Bioinformatics Databases; Regulators of gene expression, promoters, activators and repressors; Proteins from sequence to structure; Protein folding and 3D structure anaylsis; PyMOL and CHIMERA for the 3D visualization of protein structures; Template-based prediction of 3D structure of proteins; Molecular docking of drug candidates onto proteins, Cell signaling pathways; Signaling pathways related data resources; KEGG, STRING based pathway analysis, Signaling pathways in Cancer, immunology and development. |
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| Course Syllabus | | Week | Subject | Related Notes / Files | | Week 1 | Types of biomolecules in signaling pathways and signal regulatory mechanisms | | | Week 2 | Intracellular compartments and signaling networks | | | Week 3 | Pathway analyses using genomics and transcriptomics data | | | Week 4 | Examples of interactomics analysis tools | | | Week 5 | Examples of metabolomics and integrated analysis tools | | | Week 6 | Examples of systems pharmacology data sources | | | Week 7 | Examples of systems pharmacology analysis tools | | | Week 8 | MidTerm | | | Week 9 | Introduction to biological macromolecules and structures | | | Week 10 | Protein bioinformatics databases and resources, EXPASY | | | Week 11 | UniProt protein knowledgebase for diverse bioinformatics analyses | | | Week 12 | Regulators of gene expression, promoters, activators and repressors | | | Week 13 | Protein folding, from sequence to structure;3D structure anaylsis; PDB database | | | Week 14 | PyMOL and CHIMERA for 3D structure analysis of proteins | | | Week 15 | Molecular docking via AutoDock Vina | | | Week 16 | Final exam | | | |
| 1 | Juang, T. 2018; Computational Sytems Biology, 1. Baskı, Humana Press. | | | 2 | Mager, DE., Kimko HHC. 2016; Systems Pharmacology and Pharmacodynamics, Springer | | | 3 | Cathy, HW., Cecilia, NA, Karen E.R. 2017; Protein Bioinformatics, Humana Press. | | | |
| 1 | Bizzari, M. 2018; Systems Biology, 1. baskı, Humana Press. | | | 2 | Manca, D. 2018; Quantitative systems Pharmacology, 1. Baskı, Elsevier. | | | |
| Method of Assessment | | Type of assessment | Week No | Date | Duration (hours) | Weight (%) | | Mid-term exam | 8 | 08/04/2019 | 2 | 30 | | Homework/Assignment/Term-paper | 12 | 13/05/2019 | 2 | 20 | | End-of-term exam | 14 | 27/05/2019 | 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 | 4 | 14 | 56 | | Sınıf dışı çalışma | 5 | 14 | 70 | | Arasınav için hazırlık | 2 | 6 | 12 | | Arasınav | 2 | 1 | 2 | | Ödev | 3 | 14 | 42 | | Dönem sonu sınavı için hazırlık | 2 | 16 | 32 | | Dönem sonu sınavı | 2 | 1 | 2 | | Diğer 1 | 4 | 14 | 56 | | Total work load | | | 272 |
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