Molecular Modeling and Protein Structure Prediction
- Dersin Düzeyi: Lisans
- Tasarlanan Ders Kodu: 2190433
- Öğretim Türü: Örgün Öğretim (Normal Öğretim)
- Dersin Kapsamı: Teorik ve Uygulama
- Akademik Yıl: 2010 - 2011
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Ders İçeriği:
Course objectives: Proteins are fundamental components of all living cells. They exhibit a vast amount of chemical and structural diversity, enabling them to carry out an extraordinarily diverse range of biological functions. Identifying a protein's 3D conformation, or structure, is key to understanding its biological function. This also opens the way for the design and development of new bioactive agents and devices to treat a disease. Thus this course aims to teach the basic principles of 3D modeling and protein structure prediction so the student can select the programs and algorithms suitable for their studies.
Course Outline :
Week 1. Introduction
Week 2. Protein Structure
Conformational Properties of Proteins
Types of Secondary Structural Elements
Classification of Protein Structures
Inference of Function from Structure
Homologous Proteins
Week 3. Methods to Determine 3D Protein Structure
CD
X-ray
NMR
Modeling Protein Structures Based on Density Maps at Intermediate Resolutions
Week 4. Ab initio Protein Modeling
The Energy of a Protein Configuration
Energy Minimization
Molecular Dynamics
Example for Small Molecule Modeling
Secondary Structure Prediction
Ramachandran Plots
Solution effects
Weeks 5-6. Comparative Protein Modeling (Homology Modeling)
Knowledge-Based Protein Modeling
Procedures for Sequence Alignments
Atom-by-Atom Superposition
Membrane Proteins
Week 7. Tools and Software Used for Modeling
Blast
Alignment tools
Secondary structure prediction algoritms
The PDB Protein Structure Data Archive
Modeller
Weeks 8-9. Techniques to Refine modeling
Y2H
Crosslinking
Fluorescence techniques
Molecular Dynamics
Monte Carlo Simulations
Other Biochemical and biophysical techniques to study protein-protein interactions.
Week 10. Threading (Prof. Dr. Tolga Can)
Week 11. Virtual Screening and Docking
Modeling of the Ligand
Hydrogen Bonding Network
Week 12. Scope and Limits of Molecular Docking
Ligand-Binding Site Complexes
Protein Contact Map Prediction
Week 13. Rational Drug Design
Biochemical and Pharmacological Description of the Problem
The Design of New Ligands
Experimental Validation of the Designed Ligand
Week 14. Analysis of Protein-Ligand Complexes