Akademik Veri Yönetim Sistemi
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
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